Universal donor cells

ABSTRACT

Genetically modified cells that are compatible with multiple subjects, e.g., universal donor cells, and methods of generating said genetic modified cells are provided herein. The universal donor cells comprise at least one genetic modification within or near at least one gene that encodes a survival factor, wherein the genetic modification comprises an insertion of a polynucleotide encoding a tolerogenic factor. The universal donor cells may further comprise at least one genetic modification within or near a gene that encodes one or more MHC-I or MHC-II human leukocyte antigens or a component or a transcriptional regulator of a MHC-I or MHC-II complex, wherein said genetic modification comprises an insertion of a polynucleotide encoding a second tolerogenic factor.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.17/013,154, filed Sep. 4, 2020, which claims the benefit of U.S.Provisional Application No. 62/896,473, filed Sep. 5, 2019, and U.S.Provisional Application No. 62/979,771, filed Feb. 21, 2020, thedisclosure of each is hereby incorporated by reference in its entirety.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING

This application contains a Sequence Listing that has been submitted inASCII format via EFS-Web and is hereby incorporated by reference in itsentirety. The ASCII copy, created on Sep. 2, 2020, is namedCT124-US1-100867-667135-Sequence-Listing ST25.txt, and is about 53,000bytes in size.

FIELD OF THE INVENTION

The invention relates to the field of gene editing and, in someembodiments, to genetic modifications for the purposes of generatingcells that are compatible with multiple subjects, e.g., universal donorcells.

BACKGROUND

Various approaches have been proposed to overcome allogeneic rejectionof transplanted or engrafted cells including HLA-matching, blockingpathways that trigger T-cell activation with antibodies, use of acocktail of immune suppressive drugs, and autologous cell therapy.Another strategy to dampen graft rejection involves minimization ofallogenic differences between transplanted or engrafted cells and therecipient. The cell surface-expressed human leukocyte antigens (HLAs),molecules encoded by genes located in the human major histocompatibilitycomplex on chromosome 6, are the major mediators of immune rejection.Mismatch of a single HLA gene between the donor and subject can cause arobust immune response (Fleischhauer K. et al. “Bone marrow-allograftrejection by T lymphocytes recognizing a single amino acid difference inHLA-B44,” N Engl J Med., 1990, 323:1818-1822). HLA genes are dividedinto MHC class I (MHC-I) and MHC class II (MHC-II). MHC-I genes (HLA-A,HLA-B, and HLA-C) are expressed in almost all tissue cell types,presenting “non-self” antigen-processed peptides to CD8+ T cells,thereby promoting their activation to cytolytic CD8+T cells.Transplanted or engrafted cells expressing “non-self” MHC-I moleculeswill cause a robust cellular immune response directed at these cells andultimately resulting in their demise by activated cytolytic CD8+ Tcells. MHC-I proteins are intimately associated withbeta-2-microglobulin (B2M) in the endoplasmic reticulum, which isessential for forming functional MHC-I molecules on the cell surface.

In contrast to the wide cellular expression of MHC-I genes, expressionof MHC-II genes is restricted to antigen-presenting cells such asdendritic cells, macrophages, and B cells. HLA antigen genes are themost polymorphic genes observed in the human genome (Rubinstein P., “HLAmatching for bone marrow transplantation—how much is enough?” N Engl JMed., 2001, 345:1842-1844). The generation of a “universal donor” cellthat is compatible with any HLA genotype provides an alternativestrategy that could resolve the immune rejection and associatedeconomical costs of current methodologies for immune evasion.

To generate such a line of universal donor cell(s), one previousapproach has been to functionally disrupt the expression of MHC-I andMHC-II class genes. This could be achieved through genetic disruption,e.g., of both genetic alleles encoding the MHC-I light chain, B2M. Theresulting B2M-null cell line and its derivatives would be expected toexhibit greatly reduced surface MHC-I and thus, reduced immunogenicityto allogeneic CD8+ T cells. The transcription activator-like effectornuclease (TALEN) targeting approach has been used to generateB2M-deficient hESC lines by deletion of a few nucleotides in exon 2 ofthe B2M gene (Lu, P. et al., “Generating hypoimmunogenic human embryonicstem cells by the disruption of beta 2-microglobulin,” Stem Cell Rev.2013, 9:806-813). Although the B2M-targeted hESC lines appeared to besurface HLA-I deficient, they were found to still contain mRNAs specificfor B2M and MHC-I. The B2M and MHC-I mRNAs were expressed at levelsequivalent to those of untargeted hESCs (both constitutive and IFN-ginduced). Thus, concern exists that these TALEN B2M-targeted hESC linesmight express residual cell surface MHC-I that would be sufficient tocause immune rejection, such as has been observed with B2M2/2 mousecells that also express B2M mRNA (Gross, R. and Rappuoli, R. “Pertussistoxin promoter sequences involved in modulation,” Proc Natl Acad Sci,1993, 90:3913-3917). Although the TALEN B2M targeted hESC lines were notexamined for off-target cleavage events, the occurrence of nonspecificcleavage when using TALENs remains a significant issue that would imposea major safety concern on their clinical use (Grau, J. et al.“TALENoffer: genome-wide TALEN off-target prediction,” Bioinformatics,2013, 29:2931-2932; Guilinger J. P. et al. “Broad specificity profilingof TALENs results in engineered nucleases with improved DNA-cleavagespecificity,” Nat Methods 2014, 11:429-435). Further, another reportgenerated IPS cells that escaped allogeneic recognition by knocking outa first B2M allele and knocking in a HLA-E gene at a second B2M allele,which resulted in surface expression of HLA-E dimers or trimers in theabsence of surface expression of HLA-A, HLA-B, or HLA-C (Gornalusse, G.G. et al., “HLA-E-expressing pluripotent stem cells escape allogeneicresponses and lysis by NK cells,” Nature Biotechnology, 2017, 35,765-773).

A potential limitation of some of the above strategies are that MHCclass I-negative cells are susceptible to lysis by natural killer (NK)cells as HLA molecules serve as major ligand inhibitors to naturalkiller (NK) cells. Host NK cells have been shown to eliminatetransplanted or engrafted B2M−/− donor cells, and a similar phenomenonoccurs in vitro with MHC class-I-negative human leukemic lines (Bix, M.et al., “Rejection of class I MHC-deficient haemopoietic cells byirradiated MHC-matched mice,” Nature, 1991, 349, 329-331; Zarcone, D. etal., “Human leukemia-derived cell lines and clones as models formechanistic analysis of natural killer cell-mediated cytotoxicity,”Cancer Res. 1987, 47, 2674-2682). Thus, there exists a need to improveupon previous methods to generate universal donor cells that can evadethe immune response as well as a need to generate cells that can survivepost-engraftment. As described herein, cell survival post-engraftmentmay be mediated by a host of other pathways independent of allogeneicrejection e.g., hypoxia, reactive oxygen species, nutrient deprivation,and oxidative stress. Also as described herein, genetic introduction ofsurvival factors (genes and/or proteins) may help cells to survivepost-engraftment. As described herein, a universal donor cell line maycombine properties that address both allogeneic rejection and survivalpost-engraftment.

SUMMARY

In some aspects, the present disclosure encompasses a method forgenerating a universal donor cell. The method comprises delivering to acell (a) a site-directed nuclease targeting a site within or near a genethat encodes a survival factor, and (b) a nucleic acid comprising anucleotide sequence encoding a tolerogenic factor that is flanked by (i)a nucleotide sequence homologous with a region located left of thetarget site of (a) and (ii) a nucleotide sequence homologous with aregion located right of the target site of (a), wherein thesite-directed nuclease cleaves the target site of (a) and the nucleicacid of (b) is inserted at a site that partially overlaps, completelyoverlaps, or is contained within, the site of (a), thereby generating auniversal donor cell, wherein the universal donor cell has increasedcell survival compared to a cell in which the nucleic acid of (b) hasnot been inserted.

In some embodiments, the survival factor is TXNIP, ZNF143, FOXO1, JNK,or MANF, and the tolerogenic factor is PD-L1, HLA-E, HLA-G, CTLA-4, orCD47. In specific embodiments, the survival factor is TXNIP and thetolerogenic factor is HLA-E. In embodiments in which the site-directednuclease is a CRISPR system comprising a CRISPR nuclease and a guide RNA(gRNA), the CRISPR nuclease is a Type II Cas9 nuclease or a Type V Cfp1nuclease, and the CRISPR nuclease is linked to at least one nuclearlocalization signal. In some embodiments, the gRNA targets apolynucleotide sequence chosen from SEQ ID NOS: 15-24 or 45-54, and (i)consists essentially of a nucleotide sequence of SEQ ID NO: 25 and (ii)consists essentially of a nucleotide sequence of SEQ ID NO: 32.

In some embodiments, the method further comprises delivering to the cell(c) a site-directed nuclease targeting a site within or near a gene thatencodes one or more of a MHC-I or MHC-II human leukocyte antigens or acomponent or a transcriptional regulator of a MHC-I or MHC-II complex,and (d) a nucleic acid comprising a nucleotide sequence encoding atolerogenic factor that is flanked by (iii) a nucleotide sequencehomologous with a region located left of the target site of (c) and a(iv) nucleotide sequence homologous with a region located right of thetarget site of (c), wherein the tolerogenic factor of (d) differs fromthe tolerogenic factor (b), wherein the site-directed nuclease cleavesthe target site of (c) and the nucleic acid of (d) is inserted at a sitethat partially overlaps, completely overlaps, or is contained within,the site of (c), wherein the universal donor cell has increased immuneevasion and/or cell survival compared to a cell in which the nucleicacid of (d) has not been inserted.

In some embodiments, the gene that encodes the one or more MHC-I orMHC-II human leukocyte antigens or the component or the transcriptionalregulator of the MHC-I or MHC-II complex is a MHC-I gene chosen fromHLA-A, HLA-B, or HLA-C, a MHC-II gene chosen from HLA-DP, HLA-DM,HLA-DOA, HLA-DOB, HLA-DQ, or HLA-DR, or a gene chosen from B2M, NLRC5,CIITA, RFX5, RFXAP, or RFXANK, and the tolerogenic factor is PD-L1,HLA-E, HLA-G, CTLA-4, or CD47. In specific embodiments, the gene thatencodes the one or more MHC-I or MHC-II human leukocyte antigens or thecomponent or the transcriptional regulator of the MHC-I or MHC-IIcomplex is B2M, and the tolerogenic factor is PD-L1. In embodiments inwhich the site-directed nuclease is a CRISPR system comprising a CRISPRnuclease and a gRNA, the CRISPR nuclease is a Type II Cas9 nuclease or aType V Cfp1 nuclease, and the CRISPR nuclease is linked to at least onenuclear localization signal. In some embodiments, the gRNA targets apolynucleotide sequence chosen from SEQ ID NOS: 1-3 or 35-44, and (iii)consists essentially of a nucleotide sequence of SEQ ID NO: 7, and (iv)consists essentially of a nucleotide sequence of SEQ ID NO: 13.

In some embodiments, the nucleotide sequence encoding a tolerogenicfactor of (b) and (d) is operably linked to an exogenous promoter. Theexogenous promoter can be chosen from a constitutive, inducible,temporal-, tissue-, or cell type-specific promoter. In some embodiments,the exogenous promoter is a CMV, EFla, PGK, CAG, or UBC promoter. Inspecific embodiments, the exogenous promoter is a CAG promoter.

The present disclosure also encompasses the universal donor cellsgenerated by the methods disclosed herein. In some embodiments, the cellis a mammalian cell. In some embodiments, the cell is a human cell. Insome embodiments, the cell is a stem cell. In some embodiments, the cellis a pluripotent stem cell (PSC), an embryonic stem cell (ESC), an adultstem cell (ASC), an induced pluripotent stem cell (iPSC), or ahematopoietic stem and progenitor cell (HSPC) (also called ahematopoietic stem cell (HSC)). In some embodiments, the cell is adifferentiated cell. In some embodiments, the cell is a somatic cell.

In general, the universal donor cells disclosed herein are capable ofbeing differentiated into lineage-restricted progenitor cells or fullydifferentiated somatic cells. In some embodiments, thelineage-restricted progenitor cells are pancreatic endoderm progenitors,pancreatic endocrine progenitors, mesenchymal progenitor cells, muscleprogenitor cells, blast cells, hematopoietic progenitor cells, or neuralprogenitor cells, and the fully differentiated somatic cells areendocrine secretory cells such as pancreatic beta cells, epithelialcells, endodermal cells, macrophages, hepatocytes, adipocytes, kidneycells, blood cells, or immune system cells. In some embodiments, thefully differentiated somatic cells are cardiomyocytes.

A further aspect of the present disclosure provides a method fortreating a subject in need thereof, wherein the method comprisesobtaining or having obtained the universal donor cells as disclosedherein following differentiation into lineage-restricted progenitorcells or fully differentiated somatic cells, and administering thelineage-restricted progenitor cells or fully differentiated somaticcells to the subject. Also provided is a method of obtaining cells foradministration to a subject in need thereof, the method comprisingobtaining or having obtained the universal donor cells as disclosedherein, and maintaining the universal donor cells for a time and underconditions sufficient for the cells to differentiate intolineage-restricted progenitor cells or fully differentiated somaticcells. In some embodiments, the subject is a human who has, is suspectedof having, or is at risk for a disease. In some embodiments, the diseaseis a genetically inheritable disease.

Still another aspect of the present disclosure encompasses a gRNAtargeting a polynucleotide sequence chosen from SEQ ID NO: 15-24 or45-54.

While the disclosure is susceptible to various modifications andalternative forms, specific embodiments thereof are shown by way ofexample in the drawings and will herein be described in detail. Itshould be understood, however, that the drawings and detaileddescription presented herein are not intended to limit the disclosure tothe particular embodiments disclosed, but on the contrary, the intentionis to cover all modifications, equivalents, and alternatives fallingwithin the spirit and scope of the present disclosure as defined by theappended claims.

Other features and advantages of this disclosure will become apparent inthe following detailed description of embodiments of this invention,taken with reference to the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows TIDE analysis of B2M gRNA cutting in CyT49 cells. B2M-1,B2M-2, and B2M-3 gRNAs were tested.

FIGS. 2A-2B show flow cytometry assessment of B2M expression with andwithout IFN-γ in WT CyT49 cells (FIG. 2A) and B2M KO CyT49 cells (FIG.2B).

FIG. 3 shows the plasmid map of B2M-CAGGS-PD-L1 donor vector for HDR.

FIG. 4 shows flow cytometry analysis for pluripotency of B2M KO/PD-L1 KICyT49 stem cells. The derived clones were >99% double positive for OCT4and SOX2, two transcription factors vital for pluripotency. IgG was usedas a negative control.

FIGS. 5A-5B show the flow cytometry analysis of WT CyT49 (FIG. 5A) and aB2M KO/PD-L1 KI (FIG. 5B) derived stem cell clones. WT cells upregulateB2M expression in response to IFNγ. B2M KO/PD-L1 KI clones fully expressPD-L1 and do not express B2M with or without IFNγ treatment. NT-1=notreatment. INTG-1=50 ng/mL IFNγ 48 hour treated cells.

FIG. 6 shows flow cytometry for FOXA2 and SOX17 at Stage 1 (DefinitiveEndoderm) cells differentiated from wild type CyT49, PD-L1 KI/B2M KO, orB2M KO CyT49 cells.

FIG. 7 shows quantitative percentage of FOXA2 and SOX17 expression inStage 1 (Definitive Endoderm) cells differentiated from wild type, PD-L1KI/B2M KO, or B2M KO cells.

FIG. 8 shows quantitative percentage of CHGA, PDX1 and NKX6.1 expressionin Stage 4 (PEC) cells differentiated from wild type, PD-L1 KI/B2M KO,or B2M KO cells.

FIG. 9 shows heterogeneous populations of cells at Stage 4 (PEC).

FIG. 10 show selected gene expression over differentiation time coursein cells differentiated from wild type, PD-L1 KI/B2M KO, or B2M KOcells.

FIGS. 11A-11F show selected gene expression over differentiation timecourse in cells differentiated from wild type, PD-L1 KI/B2M KO, or B2MKO cells. FIG. 11A shows B2M expression in wild type cells. FIG. 11Bshows B2M expression in B2M KO cells. FIG. 11C shows B2M expression inPD-L1 KI/B2M KO cells. FIG. 11D shows PD-L1 expression in wild typecells. FIG. 11E shows PD-L1 expression in B2M KO cells. FIG. 11F showsPD-L1 expression in PD-L1 KI/B2M KO cells.

FIGS. 12A-12F show MHC class I and class II expression at PEC stage incells differentiated from wild type, PD-L1 KI/B2M KO, or B2M KO cells.FIG. 12A shows MHC class I expression in wild type cells. FIG. 12B showsMHC class I expression in B2M KO cells.

FIG. 12C shows MHC class I expression in PD-L1 KI/B2M KO cells. FIG. 12Dshows MHC class II PD-L1 expression in wild type cells. FIG. 12E showsMHC class II expression in B2M KO cells. FIG. 12F shows MHC class IIexpression in PD-L1 KI/B2M KO cells

FIG. 13 shows TIDE analysis of TXNIP gRNA cutting in TC1133 hiPSCs.Guide T5 appeared to be best at cutting at exon 1.

FIG. 14 shows the plasmid map of TXNIP-CAGGS-HLA-E donor vector for HDR.

FIG. 15 shows flow cytometry analysis for pluripotency of B2M KO/PD-L1KI and TXNIP KO/HLA-E KI CyT49 stem cells. The derived clones were >99%double positive for OCT4 and SOX2, two transcription factors vital forpluripotency. The clones also do not express B2M. The clones do notexpress MHC-I.

FIG. 16 shows flow cytometry analysis for pluripotency of B2M KO/PD-L1KI and TXNIP KO/HLA-E KI CyT49 stem cells. The derived clones expressPD-L1 and HLA-E after undergoing differentiation to Stage 6 (immaturebeta cells). IgG was used as a negative control.

FIG. 17 shows quantitative percentage of CHGA, PDX1 and NKX6.1expression in Stage 4 (PEC) cells differentiated from wild type, B2M KO,PD-L1 KI/B2M KO (V1A), or TXNIP KO/HLA-E KI (V1B) hESCs.

FIGS. 18A-18B show selected gene expression over differentiation timecourse in TXNIP KO cells (FIG. 18A) or TXNIP KO/HLA-E KI (V1B) (FIG.18B) cells.

FIGS. 19A-19B show flow cytometry analysis for T-cell activation usingthe CFSE proliferation assay. Human primary CD3+ T cells wereco-incubated with PEC derived from WT, B2M KO, B2M KO/PD-L1 KI, or B2MKO/PD-L1 KI+TXNIP KO/HLA-E KI CyT49 clones (FIG. 19A). FIG. 19Bsummarizes T-cell activation in the various cells. One-way ANOVA (α=0.05with Dunnett's multiple comparisons test) with “CFSE-T alone” set ascontrol. *, p<0.05; **, p<0.01; ***, p<0.001; ****, p<0.0001. n. s.=notsignificant.

FIG. 20 shows selected gene expression over a differentiation timecourse of cells differentiated from TXNIP KO cells.

FIG. 21 shows flow cytometry assessment of PDX1 and NKX6.1 expression inPEC cells differentiated from TXNIP KO cells.

FIG. 22 shows the morphology of the various B2M KO/PD-L1 KI and TXNIPKO/HLA-E KI clones (“56-V1B-H9,” “S6-V1B-3B11,” “S6-V1B-1G7,” and“S6-V1B-3C2”) compared to wild-type (“WT”) and non-cutting guide control(“NCG #1”) cells after differentiation to Stage 6.

FIGS. 23A-23F show selected gene expression of the clones afterdifferentiation to Stage 6. FIG. 23A shows the selected gene expressionover a differentiation time course of cells differentiated from anexemplary B2M KO/PD-L1 KI and TXNIP KO/HLA-E KI clone. FIGS. 23B-23Fshow gene expression of INS (FIG. 23B), NKX6.1 (FIG. 23C), GCG (FIG.23D), SST (FIG. 23E), and GCK (FIG. 23F) in wild-type cells (“S6-Cyt49WT”), non-cutting guide control (“S6-NCG #1”) cells, and various B2MKO/PD-L1 KI and TXNIP KO/HLA-E KI clones (“S6-V1B-H9,” “S6-V1B-3B11,”“S6-V1B-1G7,” and “S6-V1B-3C2”) that were differentiated to Stage 6 withundifferentiated B2M KO/PD-L1 KI and TXNIP KO/HLA-E KI clone(“ES-V1B-H9”) and wild-type islets (“Islets”) as controls.

FIGS. 24A-24B show flow cytometry assessment of INS and GCG expression(FIG. 24A) and INS and NKX6.1 expression (FIG. 24B) in Stage 6 cellsdifferentiated from a B2M KO/PD-L1 KI and TXNIP KO/HLA-E KI clone.

FIGS. 25A-25B show the percentage of INS expression (FIG. 25A) andNKX6.1 expression (FIG. 25B) in Stage 6 cells differentiated fromwild-type cells (“S6-WT”), non-cutting guide control cells (“S6-NCG#1”), and two B2M KO/PD-L1 KI and TXNIP KO/HLA-E KI clones (“56-V1B003”and “V1B-H9”).

FIG. 26A shows flow cytometry assessment of PDX1 and NKX6.1 expressionin Stage 4 cells differentiated from clone 1 (B2M KO/PD-L1 KI and TXNIPKO/HLA-E KI) cells with different seeding densities.

FIG. 26B shows flow cytometry assessment for PD-L1 and HLA-E expressionin Stage 4 cells differentiated from clone 1 (B2M KO/PD-L1 KI and TXNIPKO/HLA-E KI) cells.

FIGS. 27A-27C show the characterization analysis of a seed clonedifferentiated to PEC stage. FIG. 27A shows the morphology, FIG. 27Bshows selected gene expression over a differentiation time course, andFIG. 27C shows the percentage of CHGA⁻/NKX6.1⁺/PDX1⁺ expressing cells inthe differentiated population.

FIG. 28 shows selected gene expression over a differentiation timecourse of cells differentiated from TXNIP KO/HLA-E KI clones.

DETAILED DESCRIPTION I. Definitions

Deletion: As used herein, the term “deletion”, which may be usedinterchangeably with the terms “genetic deletion” or “knock-out”,generally refers to a genetic modification wherein a site or region ofgenomic DNA is removed by any molecular biology method, e.g., methodsdescribed herein, e.g., by delivering to a site of genomic DNA anendonuclease and at least one gRNA. Any number of nucleotides can bedeleted. In some embodiments, a deletion involves the removal of atleast one, at least two, at least three, at least four, at least five,at least ten, at least fifteen, at least twenty, or at least 25nucleotides. In some embodiments, a deletion involves the removal of10-50, 25-75, 50-100, 50-200, or more than 100 nucleotides. In someembodiments, a deletion involves the removal of an entire target gene,e.g., a B2M gene. In some embodiments, a deletion involves the removalof part of a target gene, e.g., all or part of a promoter and/or codingsequence of a B2M gene. In some embodiments, a deletion involves theremoval of a transcriptional regulator, e.g., a promoter region, of atarget gene. In some embodiments, a deletion involves the removal of allor part of a coding region such that the product normally expressed bythe coding region is no longer expressed, is expressed as a truncatedform, or expressed at a reduced level. In some embodiments, a deletionleads to a decrease in expression of a gene relative to an unmodifiedcell.

Endonuclease: As used herein, the term “endonuclease” generally refersto an enzyme that cleaves phosphodiester bonds within a polynucleotide.In some embodiments, an endonuclease specifically cleaves phosphodiesterbonds within a DNA polynucleotide. In some embodiments, an endonucleaseis a zinc finger nuclease (ZFN), transcription activator like effectornuclease (TALEN), homing endonuclease (HE), meganuclease, MegaTAL, or aCRISPR-associated endonuclease. In some embodiments, an endonuclease isa RNA-guided endonuclease. In certain aspects, the RNA-guidedendonuclease is a CRISPR nuclease, e.g., a Type II CRISPR Cas9endonuclease or a Type V CRISPR Cpf1 endonuclease. In some embodiments,an endonuclease is a Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7,Cas8, Cas9 (also known as Csn1 and Csx12), Cas100, Csy1, Csy2, Csy3,Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1,Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16,CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, or Cpf1 endonuclease,or a homolog thereof, a recombination of the naturally occurringmolecule thereof, a codon-optimized version thereof, or a modifiedversion thereof, or combinations thereof. In some embodiments, anendonuclease may introduce one or more single-stranded breaks (SSBs)and/or one or more double-stranded breaks (DSBs).

Genetic modification: As used herein, the term “genetic modification”generally refers to a site of genomic DNA that has been geneticallyedited or manipulated using any molecular biological method, e.g.,methods described herein, e.g., by delivering to a site of genomic DNAan endonuclease and at least one gRNA. Example genetic modificationsinclude insertions, deletions, duplications, inversions, andtranslocations, and combinations thereof. In some embodiments, a geneticmodification is a deletion. In some embodiments, a genetic modificationis an insertion. In other embodiments, a genetic modification is aninsertion-deletion mutation (or indel), such that the reading frame ofthe target gene is shifted leading to an altered gene product or no geneproduct.

Guide RNA (gRNA): As used herein, the term “guide RNA” or “gRNA”generally refers to short ribonucleic acid that can interact with, e.g.,bind to, to an endonuclease and bind, or hybridize to a target genomicsite or region. In some embodiments, a gRNA is a single-molecule guideRNA (sgRNA). In some embodiments, a gRNA may comprise a spacer extensionregion. In some embodiments, a gRNA may comprise a tracrRNA extensionregion. In some embodiments, a gRNA is single-stranded. In someembodiments, a gRNA comprises naturally occurring nucleotides. In someembodiments, a gRNA is a chemically modified gRNA. In some embodiments,a chemically modified gRNA is a gRNA that comprises at least onenucleotide with a chemical modification, e.g., a 2′-O-methyl sugarmodification. In some embodiments, a chemically modified gRNA comprisesa modified nucleic acid backbone. In some embodiments, a chemicallymodified gRNA comprises a 2′-O-methyl-phosphorothioate residue. In someembodiments, a gRNA may be pre-complexed with a DNA endonuclease.

Insertion: As used herein, the term “insertion” which may be usedinterchangeably with the terms “genetic insertion” or “knock-in”,generally refers to a genetic modification wherein a polynucleotide isintroduced or added into a site or region of genomic DNA by anymolecular biological method, e.g., methods described herein, e.g., bydelivering to a site of genomic DNA an endonuclease and at least onegRNA. In some embodiments, an insertion may occur within or near a siteof genomic DNA that has been the site of a prior genetic modification,e.g., a deletion or insertion-deletion mutation. In some embodiments, aninsertion occurs at a site of genomic DNA that partially overlaps,completely overlaps, or is contained within a site of a prior geneticmodification, e.g., a deletion or insertion-deletion mutation. In someembodiments, an insertion occurs at a safe harbor locus. In someembodiments, an insertion involves the introduction of a polynucleotidethat encodes a protein of interest. In some embodiments, an insertioninvolves the introduction of a polynucleotide that encodes a tolerogenicfactor. In some embodiments, an insertion involves the introduction of apolynucleotide that encodes a survival factor. In some embodiments, aninsertion involves the introduction of an exogenous promoter, e.g., aconstitutive promoter, e.g., a CAG promoter. In some embodiments, aninsertion involves the introduction of a polynucleotide that encodes anoncoding gene. In general, a polynucleotide to be inserted is flankedby sequences (e.g., homology arms) having substantial sequence homologywith genomic DNA at or near the site of insertion.

Major histocompatibility complex class I (MHC-I): As used herein, theterms “Major histocompatibility complex class I” or “MHC-I” generallyrefer to a class of biomolecules that are found on the cell surface ofall nucleated cells in vertebrates, including mammals, e.g., humans; andfunction to display peptides of non-self or foreign antigens, e.g.,proteins, from within the cell (i.e. cytosolic) to cytotoxic T cells,e.g., CD8+ T cells, in order to stimulate an immune response. In someembodiments, a MHC-I biomolecule is a MHC-I gene or a MHC-I protein.Complexation of MHC-I proteins with beta-2 microglobulin (B2M) proteinis required for the cell surface expression of all MHC-I proteins. Insome embodiments, decreasing the expression of a MHC-I human leukocyteantigen (HLA) relative to an unmodified cell involves a decrease (orreduction) in the expression of a MHC-I gene. In some embodiments,decreasing the expression of a MHC-I human leukocyte antigen (HLA)relative to an unmodified cell involves a decrease (or reduction) in thecell surface expression of a MHC-I protein. In some embodiments, a MHC-Ibiomolecule is HLA-A (NCBI Gene ID No: 3105), HLA-B (NCBI Gene ID No:3106), HLA-C(NCBI Gene ID No: 3107), or B2M (NCBI Gene ID No: 567).

Major histocompatibility complex class II (MHC-II): As used herein, theterm “Major histocompatibility complex class II” or “MHC-II” generallyrefer to a class of biomolecules that are typically found on the cellsurface of antigen-presenting cells in vertebrates, including mammals,e.g., humans; and function to display peptides of non-self or foreignantigens, e.g., proteins, from outside of the cell (extracellular) tocytotoxic T cells, e.g., CD8+ T cells, in order to stimulate an immuneresponse. In some embodiments, an antigen-presenting cell is a dendriticcell, macrophage, or a B cell. In some embodiments, a MHC-II biomoleculeis a MHC-II gene or a MHC-II protein. In some embodiments, decreasingthe expression of a MHC-II human leukocyte antigen (HLA) relative to anunmodified cell involves a decrease (or reduction) in the expression ofa MHC-II gene. In some embodiments, decreasing the expression of aMHC-II human leukocyte antigen (HLA) relative to an unmodified cellinvolves a decrease (or reduction) in the cell surface expression of aMHC-II protein. In some embodiments, a MHC-II biomolecule is HLA-DPA(NCBI Gene ID No: 3113), HLA-DPB (NCBI Gene ID No: 3115), HLA-DMA (NCBIGene ID No: 3108), HLA-DMB (NCBI Gene ID No: 3109), HLA-DOA (NCBI GeneID No: 3111), HLA-DOB (NCBI Gene ID No: 3112), HLA-DQA (NCBI Gene ID No:3117), HLA-DQB (NCBI Gene ID No: 3119), HLA-DRA (NCBI Gene ID No: 3122),or HLA-DRB (NCBI Gene ID No: 3123).

Polynucleotide: As used herein, the term “polynucleotide”, which may beused interchangeably with the term “nucleic acid” generally refers to abiomolecule that comprises two or more nucleotides. In some embodiments,a polynucleotide comprises at least two, at least five at least ten, atleast twenty, at least 30, at least 40, at least 50, at least 100, atleast 200, at least 250, at least 500, or any number of nucleotides. Forexample, the polynucleotides may include at least 500 nucleotides, atleast about 600 nucleotides, at least about 700 nucleotides, at leastabout 800 nucleotides, at least about 900 nucleotides, at least about1000 nucleotides, at least about 2000 nucleotides, at least about 3000nucleotides, at least about 4000 nucleotides, at least about 4500nucleotides, or at least about 5000 nucleotides. A polynucleotide may bea DNA or RNA molecule or a hybrid DNA/RNA molecule. A polynucleotide maybe single-stranded or double-stranded. In some embodiments, apolynucleotide is a site or region of genomic DNA. In some embodiments,a polynucleotide is an endogenous gene that is comprised within thegenome of an unmodified cell or universal donor cell. In someembodiments, a polynucleotide is an exogenous polynucleotide that is notintegrated into genomic DNA. In some embodiments, a polynucleotide is anexogenous polynucleotide that is integrated into genomic DNA. In someembodiments, a polynucleotide is a plasmid or an adeno-associated viralvector. In some embodiments, a polynucleotide is a circular or linearmolecule.

Safe harbor locus: As used herein, the term “safe harbor locus”generally refers to any location, site, or region of genomic DNA thatmay be able to accommodate a genetic insertion into said location, site,or region without adverse effects on a cell. In some embodiments, a safeharbor locus is an intragenic or extragenic region. In some embodiments,a safe harbor locus is a region of genomic DNA that is typicallytranscriptionally silent. In some embodiments, a safe harbor locus is aAAVS1 (PPP1 R12C), ALB, Angptl3, ApoC3, ASGR2, CCR5, FIX (F9), G6PC,Gys2, HGD, Lp(a), Pcsk9, Serpina1, TF, or TTR locus. In someembodiments, a safe harbor locus is described in Sadelain, M. et al.,“Safe harbours for the integration of new DNA in the human genome,”Nature Reviews Cancer, 2012, Vol 12, pages 51-58.

Safety switch: As used herein, the term “safety switch” generally refersto a biomolecule that leads a cell to undergo apoptosis. In someembodiments, a safety switch is a protein or gene. In some embodiments,a safety switch is a suicide gene. In some embodiments, a safety switch,e.g., herpes simplex virus thymidine kinase (HSV-tk), leads a cell toundergo apoptosis by metabolizing a prodrug, e.g., ganciclovir. In someembodiments, the overexpressed presence of a safety switch on its ownleads a cell to undergo apoptosis. In some embodiments, a safety switchis a p53-based molecule, HSV-tk, or inducible caspase-9.

Subject: As used herein, the term “subject” refers to a mammal. In someembodiments, a subject is non-human primate or rodent. In someembodiments, a subject is a human. In some embodiments, a subject has,is suspected of having, or is at risk for, a disease or disorder. Insome embodiments, a subject has one or more symptoms of a disease ordisorder.

Survival factor: As used herein, the term “survival factor” generallyrefers to a protein (e.g., expressed by a polynucleotide as describedherein) that, when increased or decreased in a cell, enables the cell,e.g., a universal donor cell, to survive after transplantation orengraftment into a host subject at higher survival rates relative to anunmodified cell. In some embodiments, a survival factor is a humansurvival factor. In some embodiments, a survival factor is a member of acritical pathway involved in cell survival. In some embodiments, acritical pathway involved in cell survival has implications on hypoxia,reactive oxygen species, nutrient deprivation, and/or oxidative stress.In some embodiments, the genetic modification, e.g., deletion orinsertion, of at least one survival factor enables a universal donorcell to survive fora longer time period, e.g., at least 1.05, at least1.1, at least 1.25, at least 1.5, at least 2, at least 3, at least 4, atleast 5, at least 10, at least 20, or at least 50 times longer timeperiod, than an unmodified cell following engraftment. In someembodiments, a survival factor is ZNF143 (NCBI Gene ID No: 7702), TXNIP(NCBI Gene ID No: 10628), FOXO1 (NCBI Gene ID No: 2308), JNK (NCBI GeneID No: 5599), or MANF (NCBI Gene ID No: 7873). In some embodiments, asurvival factor is inserted into a cell, e.g., a universal donor cell.In some embodiments, a survival factor is deleted from a cell, e.g., auniversal donor cell. In some embodiments, an insertion of apolynucleotide that encodes MANF enables a cell, e.g., a universal donorcell, to survive after transplantation or engraftment into a hostsubject at higher survival rates relative to an unmodified cell. In someembodiments, a deletion or insertion-deletion mutation within or near aZNF143, TXNIP, FOXO1, or JNK gene enables a cell, e.g., a universaldonor cell, to survive after transplantation or engraftment into a hostsubject at higher survival rates relative to an unmodified cell.

Tolerogenic factor: As used herein, the term “tolerogenic factor”generally refers to a protein (e.g., expressed by a polynucleotide asdescribed herein) that, when increased or decreased in a cell, enablesthe cell, e.g., a universal donor cell, to inhibit or evade immunerejection after transplantation or engraftment into a host subject athigher rates relative to an unmodified cell. In some embodiments, atolerogenic factor is a human tolerogenic factor. In some embodiments,the genetic modification of at least one tolerogenic factor (e.g., theinsertion or deletion of at least one tolerogenic factor) enables acell, e.g., a universal donor cell. to inhibit or evade immune rejectionwith rates at least 1.05, at least 1.1, at least 1.25, at least 1.5, atleast 2, at least 3, at least 4, at least 5, at least 10, at least 20,or at least 50 times higher than an unmodified cell followingengraftment. In some embodiments, a tolerogenic factor is HLA-E (NCBIGene ID No: 3133), HLA-G (NCBI Gene ID No: 3135), CTLA-4 (NCBI Gene IDNo: 1493), CD47 (NCBI Gene ID No: 961), or PD-L1 (NCBI Gene ID No:29126). In some embodiments, a tolerogenic factor is inserted into acell, e.g., a universal donor cell. In some embodiments, a tolerogenicfactor is deleted from a cell, e.g., a universal donor cell. In someembodiments, an insertion of a polynucleotide that encodes HLA-E, HLA-G,CTLA-4, CD47, and/or PD-L1 enables a cell, e.g., a universal donor cell,to inhibit or evade immune rejection after transplantation orengraftment into a host subject.

Transcriptional regulator of MHC-I or MHC-II: As used herein, the term“transcriptional regulator of MHC-I or MHC-II” generally refers to abiomolecule that modulates, e.g., increases or decreases, the expressionof a MHC-I and/or MHC-II human leukocyte antigen. In some embodiments, abiomolecule is a polynucleotide, e.g., a gene, or a protein. In someembodiments, a transcriptional regulator of MHC-I or MHC-II willincrease or decrease the cell surface expression of at least one MHC-Ior MHC-II protein. In some embodiments, a transcriptional regulator ofMHC-I or MHC-II will increase or decrease the expression of at least oneMHC-I or MHC-II gene. In some embodiments, the transcriptional regulatoris CIITA (NCBI Gene ID No: 4261) or NLRC5 (NCBI Gene ID No: 84166). Insome embodiments, deletion or reduction of expression of CIITA or NLRC5decreases expression of at least one MHC-I or MHC-II gene.

Universal donor cell: As used herein, the term “universal donor cell”generally refers to a genetically modified cell that is less susceptibleto allogeneic rejection during a cellular transplant and/or demonstratesincreased survival after transplantation, relative to an unmodifiedcell. In some embodiments, a genetically modified cell as describedherein is a universal donor cell. In some embodiments, the universaldonor cell has increased immune evasion and/or cell survival compared toan unmodified cell. In some embodiments, the universal donor cell hasincreased cell survival compared to an unmodified cell. In someembodiments, a universal donor cell may be a stem cell. In someembodiments, a universal donor cell may be an embryonic stem cell (ESC),an adult stem cell (ASC), an induced pluripotent stem cell (iPSC), or ahematopoietic stem or progenitor cell (HSPC) (also called ahematopoietic stem cell (HSC)). In some embodiments, a universal donorcell may be a differentiated cell. In some embodiments, a universaldonor cell may be a somatic cell (e.g., immune system cells). In someembodiments, a universal donor cell is administered to a subject. Insome embodiments, a universal donor cell is administered to a subjectwho has, is suspected of having, or is at risk for a disease. In someembodiments, the universal donor cell is capable of being differentiatedinto lineage-restricted progenitor cells or fully differentiated somaticcells. In some embodiments, the lineage-restricted progenitor cells arepancreatic endoderm progenitors, pancreatic endocrine progenitors,mesenchymal progenitor cells, muscle progenitor cells, blast cells,hematopoietic progenitor cells, or neural progenitor cells. In someembodiments, the fully differentiated somatic cells are endocrinesecretory cells such as pancreatic beta cells, epithelial cells,endodermal cells, macrophages, hepatocytes, adipocytes, kidney cells,blood cells, or immune system cells. In some embodiments, the fullydifferentiated somatic cells are cardiomyocytes.

Unmodified cell: As used herein, the term “unmodified cell” refers to acell that has not been subjected to a genetic modification involving apolynucleotide or gene that encodes a MHC-I, MHC-I, transcriptionalregulator of MHC-I or MHC-II, survival factor, and/or tolerogenicfactor. In some embodiments, an unmodified cell may be a stem cell. Insome embodiments, an unmodified cell may be an embryonic stem cell(ESC), an adult stem cell (ASC), an induced pluripotent stem cell(iPSC), or a hematopoietic stem or progenitor cell (HSPC) (also called ahematopoietic stem cell (HSC)). In some embodiments, an unmodified cellmay be a differentiated cell. In some embodiments, an unmodified cellmay be selected from somatic cells (e.g., immune system cells, e.g., a Tcell, e.g., a CD8+ T cell). If a universal donor cell is compared“relative to an unmodified cell”, the universal donor cell and theunmodified cell are the same cell type or share a common parent cellline, e.g., a universal donor iPSC is compared relative to an unmodifiediPSC.

Within or near a gene: As used herein, the term “within or near a gene”refers to a site or region of genomic DNA that is an intronic orextronic component of a said gene or is located proximal to a said gene.In some embodiments, a site of genomic DNA is within a gene if itcomprises at least a portion of an intron or exon of said gene. In someembodiments, a site of genomic DNA located near a gene may be at the 5′or 3′ end of said gene (e.g., the 5′ or 3′ end of the coding region ofsaid gene). In some embodiments, a site of genomic DNA located near agene may be a promoter region or repressor region that modulates theexpression of said gene. In some embodiments, a site of genomic DNAlocated near a gene may be on the same chromosome as said gene. In someembodiments, a site or region of genomic DNA is near a gene if it iswithin 50 Kb, 40 Kb, 30 Kb, 20 Kb, 10 Kb, 5 Kb, 1 Kb, or closer to the5′ or 3′ end of said gene (e.g., the 5′ or 3′ end of the coding regionof said gene).

II. Genome Editing Methods

Genome editing generally refers to the process of modifying thenucleotide sequence of a genome, preferably in a precise orpre-determined manner. In some embodiments, genome editing methods asdescribed herein, e.g., the CRISPR-endonuclease system, may be used togenetically modify a cell as described herein, e.g., to create auniversal donor cell. In some embodiments, genome editing methods asdescribed herein, e.g., the CRISPR-endonuclease system, may be used togenetically modify a cell as described herein, e.g., to introduce atleast one genetic modification within or near at least one gene thatdecreases the expression of one or more MHC-I and/or MHC-II humanleukocyte antigens or other components of the MHC-I or MHC-II complexrelative to an unmodified cell; to introduce at least one geneticmodification that increases the expression of at least onepolynucleotide that encodes a tolerogenic factor relative to anunmodified cell; and/or to introduce at least one genetic modificationthat increases or decreases the expression of at least one gene thatencodes a survival factor relative to an unmodified cell.

Examples of methods of genome editing described herein include methodsof using site-directed nucleases to cut deoxyribonucleic acid (DNA) atprecise target locations in the genome, thereby creating single-strandor double-strand DNA breaks at particular locations within the genome.Such breaks can be and regularly are repaired by natural, endogenouscellular processes, such as homology-directed repair (HDR) andnon-homologous end joining (NHEJ), as described in Cox et al.,“Therapeutic genome editing: prospects and challenges,”, NatureMedicine, 2015, 21(2), 121-31. These two main DNA repair processesconsist of a family of alternative pathways. NHEJ directly joins the DNAends resulting from a double-strand break, sometimes with the loss oraddition of nucleotide sequence, which may disrupt or enhance geneexpression. HDR utilizes a homologous sequence, or donor sequence, as atemplate for inserting a defined DNA sequence at the break point. Thehomologous sequence can be in the endogenous genome, such as a sisterchromatid. Alternatively, the donor sequence can be an exogenouspolynucleotide, such as a plasmid, a single-strand oligonucleotide, adouble-stranded oligonucleotide, a duplex oligonucleotide or a virus,that has regions (e.g., left and right homology arms) of high homologywith the nuclease-cleaved locus, but which can also contain additionalsequence or sequence changes including deletions that can beincorporated into the cleaved target locus. A third repair mechanism canbe microhomology-mediated end joining (MMEJ), also referred to as“Alternative NHEJ,” in which the genetic outcome is similar to NHEJ inthat small deletions and insertions can occur at the cleavage site. MMEJcan make use of homologous sequences of a few base pairs flanking theDNA break site to drive a more favored DNA end joining repair outcome,and recent reports have further elucidated the molecular mechanism ofthis process; see, e.g., Cho and Greenberg, Nature, 2015, 518, 174-76;Kent et al., Nature Structural and Molecular Biology, 2015, 22(3):230-7;Mateos-Gomez et al., Nature, 2015, 518, 254-57; Ceccaldi et al., Nature,2015, 528, 258-62. In some instances, it may be possible to predictlikely repair outcomes based on analysis of potential microhomologies atthe site of the DNA break.

Each of these genome editing mechanisms can be used to create desiredgenetic modifications. A step in the genome editing process can be tocreate one or two DNA breaks, the latter as double-strand breaks or astwo single-stranded breaks, in the target locus as near the site ofintended mutation. This can be achieved via the use of endonucleases, asdescribed and illustrated herein.

CRISPR Endonuclease System

The CRISPR-endonuclease system is a naturally occurring defensemechanism in prokaryotes that has been repurposed as a RNA-guidedDNA-targeting platform used for gene editing. CRISPR systems includeTypes I, II, III, IV, V, and VI systems. In some aspects, the CRISPRsystem is a Type II CRISPR/Cas9 system. In other aspects, the CRISPRsystem is a Type V CRISPR/Cprf system. CRISPR systems rely on a DNAendonuclease, e.g., Cas9, and two noncoding RNAs—crisprRNA (crRNA) andtrans-activating RNA (tracrRNA)—to target the cleavage of DNA.

The crRNA drives sequence recognition and specificity of theCRISPR-endonuclease complex through Watson-Crick base pairing, typicallywith a ˜20 nucleotide (nt) sequence in the target DNA. Changing thesequence of the 5′ 20 nt in the crRNA allows targeting of theCRISPR-endonuclease complex to specific loci. The CRISPR-endonucleasecomplex only binds DNA sequences that contain a sequence match to thefirst 20 nt of the single-guide RNA (sgRNA) if the target sequence isfollowed by a specific short DNA motif (with the sequence NGG) referredto as a protospacer adjacent motif (PAM).

TracrRNA hybridizes with the 3′ end of crRNA to form an RNA-duplexstructure that is bound by the endonuclease to form the catalyticallyactive CRISPR-endonuclease complex, which can then cleave the targetDNA.

Once the CRISPR-endonuclease complex is bound to DNA at a target site,two independent nuclease domains within the endonuclease each cleave oneof the DNA strands three bases upstream of the PAM site, leaving adouble-strand break (DSB) where both strands of the DNA terminate in abase pair (a blunt end).

In some embodiments, the endonuclease is a Cas9 (CRISPR associatedprotein 9). In some embodiments, the Cas9 endonuclease is fromStreptococcus pyogenes, although other Cas9 homologs may be used, e.g.,S. aureus Cas9, N. meningitidis Cas9, S. thermophilus CRISPR1 Cas9, S.thermophilus CRISPR 3 Cas9, or T. denticola Cas9. In other instance s,the CRISPR endonuclease is Cpf1, e.g., L. bacterium ND2006 Cpf1 orAcidaminococcus sp. BV3L6 Cpf1. In some embodiments, the endonuclease isCas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also knownas Csn1 and Csx12), Cas100, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2,Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6,Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15,Csf1, Csf2, Csf3, Csf4, or Cpf1 endonuclease. In some embodiments,wild-type variants may be used. In some embodiments, modified versions(e.g., a homolog thereof, a recombination of the naturally occurringmolecule thereof, codon-optimized thereof, or modified versions thereof)of the preceding endonucleases may be used.

The CRISPR nuclease can be linked to at least one nuclear localizationsignal (NLS). The at least one NLS can be located at or within 50 aminoacids of the amino-terminus of the CRISPR nuclease and/or at least oneNLS can be located at or within 50 amino acids of the carboxy-terminusof the CRISPR nuclease.

Exemplary CRISPR/Cas polypeptides include the Cas9 polypeptides aspublished in Fonfara et al., “Phylogeny of Cas9 determines functionalexchangeability of dual-RNA and Cas9 among orthologous type IICRISPR-Cas systems,” Nucleic Acids Research, 2014, 42: 2577-2590. TheCRISPR/Cas gene naming system has undergone extensive rewriting sincethe Cas genes were discovered. Fonfara et al. also provides PAMsequences for the Cas9 polypeptides from various species.

Zinc Finger Nucleases

Zinc finger nucleases (ZFNs) are modular proteins comprised of anengineered zinc finger DNA binding domain linked to the catalytic domainof the type II endonuclease FokI. Because FokI functions only as adimer, a pair of ZFNs must be engineered to bind to cognate target“half-site” sequences on opposite DNA strands and with precise spacingbetween them to enable the catalytically active FokI dimer to form. Upondimerization of the FokI domain, which itself has no sequencespecificity per se, a DNA double-strand break is generated between theZFN half-sites as the initiating step in genome editing.

The DNA binding domain of each ZFN is typically comprised of 3-6 zincfingers of the abundant Cys2-His2 architecture, with each fingerprimarily recognizing a triplet of nucleotides on one strand of thetarget DNA sequence, although cross-strand interaction with a fourthnucleotide also can be important. Alteration of the amino acids of afinger in positions that make key contacts with the DNA alters thesequence specificity of a given finger. Thus, a four-finger zinc fingerprotein will selectively recognize a 12 bp target sequence, where thetarget sequence is a composite of the triplet preferences contributed byeach finger, although triplet preference can be influenced to varyingdegrees by neighboring fingers. An important aspect of ZFNs is that theycan be readily re-targeted to almost any genomic address simply bymodifying individual fingers. In most applications of ZFNs, proteins of4-6 fingers are used, recognizing 12-18 bp respectively. Hence, a pairof ZFNs will typically recognize a combined target sequence of 24-36 bp,not including the typical 5-7 bp spacer between half-sites. The bindingsites can be separated further with larger spacers, including 15-17 bp.A target sequence of this length is likely to be unique in the humangenome, assuming repetitive sequences or gene homologs are excludedduring the design process. Nevertheless, the ZFN protein-DNAinteractions are not absolute in their specificity so off-target bindingand cleavage events do occur, either as a heterodimer between the twoZFNs, or as a homodimer of one or the other of the ZFNs. The latterpossibility has been effectively eliminated by engineering thedimerization interface of the FokI domain to create “plus” and “minus”variants, also known as obligate heterodimer variants, which can onlydimerize with each other, and not with themselves. Forcing the obligateheterodimer prevents formation of the homodimer. This has greatlyenhanced specificity of ZFNs, as well as any other nuclease that adoptsthese FokI variants.

A variety of ZFN-based systems have been described in the art,modifications thereof are regularly reported, and numerous referencesdescribe rules and parameters that are used to guide the design of ZFNs;see, e.g., Segal et al., Proc Natl Acad Sci, 1999 96(6):2758-63; DreierB et al., J Mol Biol., 2000, 303(4):489-502; Liu Q et al., J Biol Chem.,2002, 277(6):3850-6; Dreier et al., J Biol Chem., 2005,280(42):35588-97; and Dreier et al., J Biol Chem. 2001,276(31):29466-78.

Transcription Activator-Like Effector Nucleases (TALENs)

TALENs represent another format of modular nucleases whereby, as withZFNs, an engineered DNA binding domain is linked to the FokI nucleasedomain, and a pair of TALENs operate in tandem to achieve targeted DNAcleavage. The major difference from ZFNs is the nature of the DNAbinding domain and the associated target DNA sequence recognitionproperties. The TALEN DNA binding domain derives from TALE proteins,which were originally described in the plant bacterial pathogenXanthomonas sp. TALEs are comprised of tandem arrays of 33-35 amino acidrepeats, with each repeat recognizing a single base pair in the targetDNA sequence that is typically up to 20 bp in length, giving a totaltarget sequence length of up to 40 bp. Nucleotide specificity of eachrepeat is determined by the repeat variable diresidue (RVD), whichincludes just two amino acids at positions 12 and 13. The bases guanine,adenine, cytosine and thymine are predominantly recognized by the fourRVDs: Asn-Asn, Asn-Ile, His-Asp and Asn-Gly, respectively. Thisconstitutes a much simpler recognition code than for zinc fingers, andthus represents an advantage over the latter for nuclease design.Nevertheless, as with ZFNs, the protein-DNA interactions of TALENs arenot absolute in their specificity, and TALENs have also benefitted fromthe use of obligate heterodimer variants of the FokI domain to reduceoff-target activity.

Additional variants of the FokI domain have been created that aredeactivated in their catalytic function. If one half of either a TALENor a ZFN pair contains an inactive FokI domain, then only single-strandDNA cleavage (nicking) will occur at the target site, rather than a DSB.The outcome is comparable to the use of CRISPR/Cas9 or CRISPR/Cpf1“nickase” mutants in which one of the Cas9 cleavage domains has beendeactivated. DNA nicks can be used to drive genome editing by HDR, butat lower efficiency than with a DSB. The main benefit is that off-targetnicks are quickly and accurately repaired, unlike the DSB, which isprone to NHEJ-mediated mis-repair.

A variety of TALEN-based systems have been described in the art, andmodifications thereof are regularly reported; see, e.g., Boch, Science,2009 326(5959):1509-12; Mak et al., Science, 2012, 335(6069):716-9; andMoscou et al., Science, 2009, 326(5959):1501. The use of TALENs based onthe “Golden Gate” platform, or cloning scheme, has been described bymultiple groups; see, e.g., Cermak et al., Nucleic Acids Res., 2011,39(12):e82; Li et al., Nucleic Acids Res., 2011, 39(14):6315-25; Weberet al., PLoS One., 2011, 6(2):e16765; Wang et al., J Genet Genomics,2014, 41(6):339-47; and Cermak T et al., Methods Mol Biol., 20151239:133-59.

Homing Endonucleases

Homing endonucleases (HEs) are sequence-specific endonucleases that havelong recognition sequences (14-44 base pairs) and cleave DNA with highspecificity—often at sites unique in the genome. There are at least sixknown families of HEs as classified by their structure, includingGIY-YIG, His-Cis box, H-N-H, PD-(D/E)xK, and Vsr-like that are derivedfrom a broad range of hosts, including eukarya, protists, bacteria,archaea, cyanobacteria and phage. As with ZFNs and TALENs, HEs can beused to create a DSB at a target locus as the initial step in genomeediting. In addition, some natural and engineered HEs cut only a singlestrand of DNA, thereby functioning as site-specific nickases. The largetarget sequence of HEs and the specificity that they offer have madethem attractive candidates to create site-specific DSBs.

A variety of HE-based systems have been described in the art, andmodifications thereof are regularly reported; see, e.g., the reviews bySteentoft et al., Glycobiology, 2014, 24(8):663-80; Belfort andBonocora, Methods Mol Biol., 2014, 1123:1-26; and Hafez and Hausner,Genome, 2012, 55(8):553-69.

MegaTAL/Tev-mTALEN/MegaTev

As further examples of hybrid nucleases, the MegaTAL platform andTev-mTALEN platform use a fusion of TALE DNA binding domains andcatalytically active HEs, taking advantage of both the tunable DNAbinding and specificity of the TALE, as well as the cleavage sequencespecificity of the HE; see, e.g., Boissel et al., Nucleic Acids Res.,2014, 42: 2591-2601; Kleinstiver et al., G3, 2014, 4:1155-65; andBoissel and Scharenberg, Methods Mol. Biol., 2015, 1239: 171-96.

In a further variation, the MegaTev architecture is the fusion of ameganuclease (Mega) with the nuclease domain derived from the GIY-YIGhoming endonuclease I-TevI (Tev). The two active sites are positioned˜30 bp apart on a DNA substrate and generate two DSBs withnon-compatible cohesive ends; see, e.g., Wolfs et al., Nucleic AcidsRes., 2014, 42, 8816-29. It is anticipated that other combinations ofexisting nuclease-based approaches will evolve and be useful inachieving the targeted genome modifications described herein.

dCas9-FokI or dCpf1-FokI and Other Nucleases

Combining the structural and functional properties of the nucleaseplatforms described above offers a further approach to genome editingthat can potentially overcome some of the inherent deficiencies. As anexample, the CRISPR genome editing system typically uses a single Cas9endonuclease to create a DSB. The specificity of targeting is driven bya 20 or 24 nucleotide sequence in the guide RNA that undergoesWatson-Crick base-pairing with the target DNA (plus an additional 2bases in the adjacent NAG or NGG PAM sequence in the case of Cas9 fromS. pyogenes). Such a sequence is long enough to be unique in the humangenome, however, the specificity of the RNA/DNA interaction is notabsolute, with significant promiscuity sometimes tolerated, particularlyin the 5′ half of the target sequence, effectively reducing the numberof bases that drive specificity. One solution to this has been tocompletely deactivate the Cas9 or Cpf1 catalytic function—retaining onlythe RNA-guided DNA binding function—and instead fusing a FokI domain tothe deactivated Cas9; see, e.g., Tsai et al., Nature Biotech, 2014, 32:569-76; and Guilinger et al., Nature Biotech., 2014, 32: 577-82. BecauseFokI must dimerize to become catalytically active, two guide RNAs arerequired to tether two FokI fusions in close proximity to form the dimerand cleave DNA. This essentially doubles the number of bases in thecombined target sites, thereby increasing the stringency of targeting byCRISPR-based systems.

As further example, fusion of the TALE DNA binding domain to acatalytically active HE, such as I-TevI, takes advantage of both thetunable DNA binding and specificity of the TALE, as well as the cleavagesequence specificity of I-TevI, with the expectation that off-targetcleavage can be further reduced.

RNA-Guided Endonucleases

The RNA-guided endonuclease systems as used herein can comprise an aminoacid sequence having at least 10%, at least 15%, at least 20%, at least30%, at least 40%, at least 50%, at least 60%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 95%, at least99%, or 100% amino acid sequence identity to a wild-type exemplaryendonuclease, e.g., Cas9 from S. pyogenes, US2014/0068797 Sequence IDNo. 8 or Sapranauskas et al., Nucleic Acids Res, 39(21): 9275-9282(2011). The endonuclease can comprise at least 70, 75, 80, 85, 90, 95,97, 99, or 100% identity to a wild-type endonuclease (e.g., Cas9 from S.pyogenes, supra) over 10 contiguous amino acids. The endonuclease cancomprise at most: 70, 75, 80, 85, 90, 95, 97, 99, or 100% identity to awild-type endonuclease (e.g., Cas9 from S. pyogenes, supra) over 10contiguous amino acids. The endonuclease can comprise at least: 70, 75,80, 85, 90, 95, 97, 99, or 100% identity to a wild-type endonuclease(e.g., Cas9 from S. pyogenes, supra) over 10 contiguous amino acids in aHNH nuclease domain of the endonuclease. The endonuclease can compriseat most: 70, 75, 80, 85, 90, 95, 97, 99, or 100% identity to a wild-typeendonuclease (e.g., Cas9 from S. pyogenes, supra) over 10 contiguousamino acids in a HNH nuclease domain of the endonuclease. Theendonuclease can comprise at least: 70, 75, 80, 85, 90, 95, 97, 99, or100% identity to a wild-type endonuclease (e.g., Cas9 from S. pyogenes,supra) over 10 contiguous amino acids in a RuvC nuclease domain of theendonuclease. The endonuclease can comprise at most: 70, 75, 80, 85, 90,95, 97, 99, or 100% identity to a wild-type endonuclease (e.g., Cas9from S. pyogenes, supra) over 10 contiguous amino acids in a RuvCnuclease domain of the endonuclease.

The endonuclease can comprise a modified form of a wild-type exemplaryendonuclease. The modified form of the wild-type exemplary endonucleasecan comprise a mutation that reduces the nucleic acid-cleaving activityof the endonuclease. The modified form of the wild-type exemplaryendonuclease can have less than 90%, less than 80%, less than 70%, lessthan 60%, less than 50%, less than 40%, less than 30%, less than 20%,less than 10%, less than 5%, or less than 1% of the nucleicacid-cleaving activity of the wild-type exemplary endonuclease (e.g.,Cas9 from S. pyogenes, supra). The modified form of the endonuclease canhave no substantial nucleic acid-cleaving activity. When an endonucleaseis a modified form that has no substantial nucleic acid-cleavingactivity, it is referred to herein as “enzymatically inactive.”

Mutations contemplated can include substitutions, additions, anddeletions, or any combination thereof. The mutation converts the mutatedamino acid to alanine. The mutation converts the mutated amino acid toanother amino acid (e.g., glycine, serine, threonine, cysteine, valine,leucine, isoleucine, methionine, proline, phenylalanine, tyrosine,tryptophan, aspartic acid, glutamic acid, asparagine, glutamine,histidine, lysine, or arginine). The mutation converts the mutated aminoacid to a non-natural amino acid (e.g., selenomethionine). The mutationconverts the mutated amino acid to amino acid mimics (e.g.,phosphomimics). The mutation can be a conservative mutation. Forexample, the mutation converts the mutated amino acid to amino acidsthat resemble the size, shape, charge, polarity, conformation, and/orrotamers of the mutated amino acids (e.g., cysteine/serine mutation,lysine/asparagine mutation, histidine/phenylalanine mutation). Themutation can cause a shift in reading frame and/or the creation of apremature stop codon. Mutations can cause changes to regulatory regionsof genes or loci that affect expression of one or more genes.

Guide RNAs

The present disclosure provides a guide RNAs (gRNAs) that can direct theactivities of an associated endonuclease to a specific target sitewithin a polynucleotide. A guide RNA can comprise at least a spacersequence that hybridizes to a target nucleic acid sequence of interest,and a CRISPR repeat sequence. In CRISPR Type II systems, the gRNA alsocomprises a second RNA called the tracrRNA sequence. In the CRISPR TypeII guide RNA (gRNA), the CRISPR repeat sequence and tracrRNA sequencehybridize to each other to form a duplex. In CRISPR Type V systems, thegRNA comprises a crRNA that forms a duplex. In some embodiments, a gRNAcan bind an endonuclease, such that the gRNA and endonuclease form acomplex. The gRNA can provide target specificity to the complex byvirtue of its association with the endonuclease. The genome-targetingnucleic acid thus can direct the activity of the endonuclease.

Exemplary guide RNAs include a spacer sequences that comprises 15-200nucleotides wherein the gRNA targets a genome location based on theGRCh38 human genome assembly. As is understood by the person of ordinaryskill in the art, each gRNA can be designed to include a spacer sequencecomplementary to its genomic target site or region. See Jinek et al.,Science, 2012, 337, 816-821 and Deltcheva et al., Nature, 2011, 471,602-607.

The gRNA can be a double-molecule guide RNA. The gRNA can be asingle-molecule guide RNA.

A double-molecule guide RNA can comprise two strands of RNA. The firststrand comprises in the 5′ to 3′ direction, an optional spacer extensionsequence, a spacer sequence and a minimum CRISPR repeat sequence. Thesecond strand can comprise a minimum tracrRNA sequence (complementary tothe minimum CRISPR repeat sequence), a 3′ tracrRNA sequence and anoptional tracrRNA extension sequence.

A single-molecule guide RNA (sgRNA) can comprise, in the 5′ to 3′direction, an optional spacer extension sequence, a spacer sequence, aminimum CRISPR repeat sequence, a single-molecule guide linker, aminimum tracrRNA sequence, a 3′ tracrRNA sequence and an optionaltracrRNA extension sequence. The optional tracrRNA extension cancomprise elements that contribute additional functionality (e.g.,stability) to the guide RNA. The single-molecule guide linker can linkthe minimum CRISPR repeat and the minimum tracrRNA sequence to form ahairpin structure. The optional tracrRNA extension can comprise one ormore hairpins.

In some embodiments, a sgRNA comprises a 20 nucleotide spacer sequenceat the 5′ end of the sgRNA sequence. In some embodiments, a sgRNAcomprises a less than a 20 nucleotide spacer sequence at the 5′ end ofthe sgRNA sequence. In some embodiments, a sgRNA comprises a more than20 nucleotide spacer sequence at the 5′ end of the sgRNA sequence. Insome embodiments, a sgRNA comprises a variable length spacer sequencewith 17-30 nucleotides at the 5′ end of the sgRNA sequence. In someembodiments, a sgRNA comprises a spacer extension sequence with a lengthof more than 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90,100, 120, 140, 160, 180, or 200 nucleotides. In some embodiments, asgRNA comprises a spacer extension sequence with a length of less than3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, or 100nucleotides.

In some embodiments, a sgRNA comprises a spacer extension sequence thatcomprises another moiety (e.g., a stability control sequence, anendoribonuclease binding sequence, or a ribozyme). The moiety candecrease or increase the stability of a nucleic acid targeting nucleicacid. The moiety can be a transcriptional terminator segment (i.e., atranscription termination sequence). The moiety can function in aeukaryotic cell. The moiety can function in a prokaryotic cell. Themoiety can function in both eukaryotic and prokaryotic cells.Non-limiting examples of suitable moieties include: a 5′ cap (e.g., a7-methylguanylate cap (m7 G)), a riboswitch sequence (e.g., to allow forregulated stability and/or regulated accessibility by proteins andprotein complexes), a sequence that forms a dsRNA duplex (i.e., ahairpin), a sequence that targets the RNA to a subcellular location(e.g., nucleus, mitochondria, chloroplasts, and the like), amodification or sequence that provides for tracking (e.g., directconjugation to a fluorescent molecule, conjugation to a moiety thatfacilitates fluorescent detection, a sequence that allows forfluorescent detection, etc.), and/or a modification or sequence thatprovides a binding site for proteins (e.g., proteins that act on DNA,including transcriptional activators, transcriptional repressors, DNAmethyltransferases, DNA demethylases, histone acetyltransferases,histone deacetylases, and the like).

In some embodiments, a sgRNA comprises a spacer sequence that hybridizesto a sequence in a target polynucleotide. The spacer of a gRNA caninteract with a target polynucleotide in a sequence-specific manner viahybridization (i.e., base pairing). The nucleotide sequence of thespacer can vary depending on the sequence of the target nucleic acid ofinterest.

In a CRISPR-endonuclease system, a spacer sequence can be designed tohybridize to a target polynucleotide that is located 5′ of a PAM of theendonuclease used in the system. The spacer may perfectly match thetarget sequence or may have mismatches. Each endonuclease, e.g., Cas9nuclease, has a particular PAM sequence that it recognizes in a targetDNA. For example, S. pyogenes Cas9 recognizes a PAM that comprises thesequence 5′-NRG-3′, where R comprises either A or G, where N is anynucleotide and N is immediately 3′ of the target nucleic acid sequencetargeted by the spacer sequence.

A target polynucleotide sequence can comprise 20 nucleotides. The targetpolynucleotide can comprise less than 20 nucleotides. The targetpolynucleotide can comprise more than 20 nucleotides. The targetpolynucleotide can comprise at least: 5, 10, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 30 or more nucleotides. The target polynucleotide cancomprise at most: 5, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30or more nucleotides. The target polynucleotide sequence can comprise 20bases immediately 5′ of the first nucleotide of the PAM.

A spacer sequence that hybridizes to a target polynucleotide can have alength of at least about 6 nucleotides (nt). The spacer sequence can beat least about 6 nt, at least about 10 nt, at least about 15 nt, atleast about 18 nt, at least about 19 nt, at least about 20 nt, at leastabout 25 nt, at least about 30 nt, at least about 35 nt or at leastabout 40 nt, from about 6 nt to about 80 nt, from about 6 nt to about 50nt, from about 6 nt to about 45 nt, from about 6 nt to about 40 nt, fromabout 6 nt to about 35 nt, from about 6 nt to about 30 nt, from about 6nt to about 25 nt, from about 6 nt to about 20 nt, from about 6 nt toabout 19 nt, from about 10 nt to about 50 nt, from about 10 nt to about45 nt, from about 10 nt to about 40 nt, from about 10 nt to about 35 nt,from about 10 nt to about 30 nt, from about 10 nt to about 25 nt, fromabout 10 nt to about 20 nt, from about 10 nt to about 19 nt, from about19 nt to about 25 nt, from about 19 nt to about 30 nt, from about 19 ntto about 35 nt, from about 19 nt to about 40 nt, from about 19 nt toabout 45 nt, from about 19 nt to about 50 nt, from about 19 nt to about60 nt, from about 20 nt to about 25 nt, from about 20 nt to about 30 nt,from about 20 nt to about 35 nt, from about 20 nt to about 40 nt, fromabout 20 nt to about 45 nt, from about 20 nt to about 50 nt, or fromabout 20 nt to about 60 nt. In some examples, the spacer sequence cancomprise 20 nucleotides. In some examples, the spacer can comprise 19nucleotides. In some examples, the spacer can comprise 18 nucleotides.In some examples, the spacer can comprise 22 nucleotides.

In some examples, the percent complementarity between the spacersequence and the target nucleic acid is at least about 30%, at leastabout 40%, at least about 50%, at least about 60%, at least about 65%,at least about 70%, at least about 75%, at least about 80%, at leastabout 85%, at least about 90%, at least about 95%, at least about 97%,at least about 98%, at least about 99%, or 100%. In some examples, thepercent complementarity between the spacer sequence and the targetnucleic acid is at most about 30%, at most about 40%, at most about 50%,at most about 60%, at most about 65%, at most about 70%, at most about75%, at most about 80%, at most about 85%, at most about 90%, at mostabout 95%, at most about 97%, at most about 98%, at most about 99%, or100%. In some examples, the percent complementarity between the spacersequence and the target nucleic acid is 100% over the six contiguous5′-most nucleotides of the target sequence of the complementary strandof the target nucleic acid. The percent complementarity between thespacer sequence and the target nucleic acid can be at least 60% overabout 20 contiguous nucleotides. The length of the spacer sequence andthe target nucleic acid can differ by 1 to 6 nucleotides, which may bethought of as a bulge or bulges.

A tracrRNA sequence can comprise nucleotides that hybridize to a minimumCRISPR repeat sequence in a cell. A minimum tracrRNA sequence and aminimum CRISPR repeat sequence may form a duplex, i.e. a base-paireddouble-stranded structure. Together, the minimum tracrRNA sequence andthe minimum CRISPR repeat can bind to an RNA-guided endonuclease. Atleast a part of the minimum tracrRNA sequence can hybridize to theminimum CRISPR repeat sequence. The minimum tracrRNA sequence can be atleast about 30%, about 40%, about 50%, about 60%, about 65%, about 70%,about 75%, about 80%, about 85%, about 90%, about 95%, or 100%complementary to the minimum CRISPR repeat sequence.

The minimum tracrRNA sequence can have a length from about 7 nucleotidesto about 100 nucleotides. For example, the minimum tracrRNA sequence canbe from about 7 nucleotides (nt) to about 50 nt, from about 7 nt toabout 40 nt, from about 7 nt to about 30 nt, from about 7 nt to about 25nt, from about 7 nt to about 20 nt, from about 7 nt to about 15 nt, fromabout 8 nt to about 40 nt, from about 8 nt to about 30 nt, from about 8nt to about 25 nt, from about 8 nt to about 20 nt, from about 8 nt toabout 15 nt, from about 15 nt to about 100 nt, from about 15 nt to about80 nt, from about 15 nt to about 50 nt, from about 15 nt to about 40 nt,from about 15 nt to about 30 nt or from about 15 nt to about 25 nt long.The minimum tracrRNA sequence can be approximately 9 nucleotides inlength. The minimum tracrRNA sequence can be approximately 12nucleotides. The minimum tracrRNA can consist of tracrRNA nt 23-48described in Jinek et al., supra.

The minimum tracrRNA sequence can be at least about 60% identical to areference minimum tracrRNA (e.g., wild type, tracrRNA from S. pyogenes)sequence over a stretch of at least 6, 7, or 8 contiguous nucleotides.For example, the minimum tracrRNA sequence can be at least about 65%identical, about 70% identical, about 75% identical, about 80%identical, about 85% identical, about 90% identical, about 95%identical, about 98% identical, about 99% identical or 100% identical toa reference minimum tracrRNA sequence over a stretch of at least 6, 7,or 8 contiguous nucleotides.

The duplex between the minimum CRISPR RNA and the minimum tracrRNA cancomprise a double helix. The duplex between the minimum CRISPR RNA andthe minimum tracrRNA can comprise at least about 1, 2, 3, 4, 5, 6, 7, 8,9, or 10 or more nucleotides. The duplex between the minimum CRISPR RNAand the minimum tracrRNA can comprise at most about 1, 2, 3, 4, 5, 6, 7,8, 9, or 10 or more nucleotides.

The duplex can comprise a mismatch (i.e., the two strands of the duplexare not 100% complementary). The duplex can comprise at least about 1,2, 3, 4, or 5 or mismatches. The duplex can comprise at most about 1, 2,3, 4, or 5 or mismatches. The duplex can comprise no more than 2mismatches.

In some embodiments, a tracrRNA may be a 3′ tracrRNA. In someembodiments, a 3′ tracrRNA sequence can comprise a sequence with atleast about 30%, about 40%, about 50%, about 60%, about 65%, about 70%,about 75%, about 80%, about 85%, about 90%, about 95%, or 100% sequenceidentity to a reference tracrRNA sequence (e.g., a tracrRNA from S.pyogenes).

In some embodiments, a gRNA may comprise a tracrRNA extension sequence.A tracrRNA extension sequence can have a length from about 1 nucleotideto about 400 nucleotides. The tracrRNA extension sequence can have alength of more than 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70,80, 90, 100, 120, 140, 160, 180, or 200 nucleotides. The tracrRNAextension sequence can have a length from about 20 to about 5000 or morenucleotides. The tracrRNA extension sequence can have a length of lessthan 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, or 100nucleotides. The tracrRNA extension sequence can comprise less than 10nucleotides in length. The tracrRNA extension sequence can be 10-30nucleotides in length. The tracrRNA extension sequence can be 30-70nucleotides in length.

The tracrRNA extension sequence can comprise a functional moiety (e.g.,a stability control sequence, ribozyme, endoribonuclease bindingsequence). The functional moiety can comprise a transcriptionalterminator segment (i.e., a transcription termination sequence). Thefunctional moiety can have a total length from about 10 nucleotides (nt)to about 100 nucleotides, from about 10 nt to about 20 nt, from about 20nt to about 30 nt, from about 30 nt to about 40 nt, from about 40 nt toabout 50 nt, from about 50 nt to about 60 nt, from about 60 nt to about70 nt, from about 70 nt to about 80 nt, from about 80 nt to about 90 nt,or from about 90 nt to about 100 nt, from about 15 nt to about 80 nt,from about 15 nt to about 50 nt, from about 15 nt to about 40 nt, fromabout 15 nt to about 30 nt, or from about 15 nt to about 25 nt.

In some embodiments, a sgRNA may comprise a linker sequence with alength from about 3 nucleotides to about 100 nucleotides. In Jinek etal., supra, for example, a simple 4 nucleotide “tetraloop” (-GAAA-) wasused (Jinek et al., Science, 2012, 337(6096):816-821). An illustrativelinker has a length from about 3 nucleotides (nt) to about 90 nt, fromabout 3 nt to about 80 nt, from about 3 nt to about 70 nt, from about 3nt to about 60 nt, from about 3 nt to about 50 nt, from about 3 nt toabout 40 nt, from about 3 nt to about 30 nt, from about 3 nt to about 20nt, from about 3 nt to about 10 nt. For example, the linker can have alength from about 3 nt to about 5 nt, from about 5 nt to about 10 nt,from about 10 nt to about 15 nt, from about 15 nt to about 20 nt, fromabout 20 nt to about 25 nt, from about 25 nt to about 30 nt, from about30 nt to about 35 nt, from about 35 nt to about 40 nt, from about 40 ntto about 50 nt, from about 50 nt to about 60 nt, from about 60 nt toabout 70 nt, from about 70 nt to about 80 nt, from about 80 nt to about90 nt, or from about 90 nt to about 100 nt. The linker of asingle-molecule guide nucleic acid can be between 4 and 40 nucleotides.The linker can be at least about 100, 500, 1000, 1500, 2000, 2500, 3000,3500, 4000, 4500, 5000, 5500, 6000, 6500, or 7000 or more nucleotides.The linker can be at most about 100, 500, 1000, 1500, 2000, 2500, 3000,3500, 4000, 4500, 5000, 5500, 6000, 6500, or 7000 or more nucleotides.

Linkers can comprise any of a variety of sequences, although in someexamples the linker will not comprise sequences that have extensiveregions of homology with other portions of the guide RNA, which mightcause intramolecular binding that could interfere with other functionalregions of the guide. In Jinek et al., supra, a simple 4 nucleotidesequence-GAAA-was used (Jinek et al., Science, 2012, 337(6096):816-821),but numerous other sequences, including longer sequences can likewise beused.

The linker sequence can comprise a functional moiety. For example, thelinker sequence can comprise one or more features, including an aptamer,a ribozyme, a protein-interacting hairpin, a protein binding site, aCRISPR array, an intron, or an exon. The linker sequence can comprise atleast about 1, 2, 3, 4, or 5 or more functional moieties. In someexamples, the linker sequence can comprise at most about 1, 2, 3, 4, or5 or more functional moieties.

In some embodiments, a sgRNA does not comprise a uracil, e.g., at the3′end of the sgRNA sequence. In some embodiments, a sgRNA does compriseone or more uracils, e.g., at the 3′end of the sgRNA sequence. In someembodiments, a sgRNA comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 uracils(U) at the 3′ end of the sgRNA sequence.

A sgRNA may be chemically modified. In some embodiments, a chemicallymodified gRNA is a gRNA that comprises at least one nucleotide with achemical modification, e.g., a 2′-O-methyl sugar modification. In someembodiments, a chemically modified gRNA comprises a modified nucleicacid backbone. In some embodiments, a chemically modified gRNA comprisesa 2′-O-methyl-phosphorothioate residue. In some embodiments, chemicalmodifications enhance stability, reduce the likelihood or degree ofinnate immune response, and/or enhance other attributes, as described inthe art.

In some embodiments, a modified gRNA may comprise a modified backbones,for example, phosphorothioates, phosphotriesters, morpholinos, methylphosphonates, short chain alkyl or cycloalkyl intersugar linkages orshort chain heteroatomic or heterocyclic intersugar linkages.

Morpholino-based compounds are described in Braasch and David Corey,Biochemistry, 2002, 41(14): 4503-4510; Genesis, 2001, Volume 30, Issue3; Heasman, Dev. Biol., 2002, 243: 209-214; Nasevicius et al., Nat.Genet., 2000, 26:216-220; Lacerra et al., Proc. Natl. Acad. Sci., 2000,97: 9591-9596; and U.S. Pat. No. 5,034,506, issued Jul. 23, 1991.

Cyclohexenyl nucleic acid oligonucleotide mimetics are described in Wanget al., J. Am. Chem. Soc., 2000, 122: 8595-8602.

In some embodiments, a modified gRNA may comprise one or moresubstituted sugar moieties, e.g., one of the following at the 2′position: OH, SH, SCH₃, F, OCN, OCH₃, OCH₃ O(CH₂)n CH₃, O(CH₂)n NH₂, orO(CH₂)n CH₃, where n is from 1 to about 10; C1 to C10 lower alkyl,alkoxyalkoxy, substituted lower alkyl, alkaryl or aralkyl; Cl; Br; CN;CF₃; OCF₃; O—, S—, or N-alkyl; O-, S-, or N-alkenyl; SOCH₃; SO₂ CH₃;ONO₂; NO₂; N₃; NH₂; heterocycloalkyl; heterocycloalkaryl;aminoalkylamino; polyalkylamino; substituted silyl; an RNA cleavinggroup; a reporter group; an intercalator; 2′-O-(2-methoxyethyl);2′-methoxy (2′-O—CH₃); 2′-propoxy (2′-OCH₂ CH₂CH₃); and 2′-fluoro(2′-F). Similar modifications may also be made at other positions on thegRNA, particularly the 3′ position of the sugar on the 3′ terminalnucleotide and the 5′ position of 5′ terminal nucleotide. In someexamples, both a sugar and an internucleoside linkage, i.e., thebackbone, of the nucleotide units can be replaced with novel groups.

Guide RNAs can also include, additionally or alternatively, nucleobase(often referred to in the art simply as “base”) modifications orsubstitutions. As used herein, “unmodified” or “natural” nucleobasesinclude adenine (A), guanine (G), thymine (T), cytosine (C), and uracil(U). Modified nucleobases include nucleobases found only infrequently ortransiently in natural nucleic acids, e.g., hypoxanthine,6-methyladenine, 5-Me pyrimidines, particularly 5-methylcytosine (alsoreferred to as 5-methyl-2′ deoxycytosine and often referred to in theart as 5-Me-C), 5-hydroxymethylcytosine (HMC), glycosyl HMC andgentobiosyl HMC, as well as synthetic nucleobases, e.g., 2-aminoadenine,2-(methylamino)adenine, 2-(imidazolylalkyl)adenine,2-(aminoalklyamino)adenine or other heterosubstituted alkyladenines,2-thiouracil, 2-thiothymine, 5-bromouracil, 5-hydroxymethyluracil,8-azaguanine, 7-deazaguanine, N6 (6-aminohexyl)adenine, and2,6-diaminopurine. Kornberg, A., DNA Replication, W. H. Freeman & Co.,San Francisco, pp 75-′7′7, 1980; Gebeyehu et al., Nucl. Acids Res. 1997,15:4513. A “universal” base known in the art, e.g., inosine, can also beincluded. 5-Me-C substitutions have been shown to increase nucleic acidduplex stability by 0.6-1.2° C. (Sanghvi, Y. S., in Crooke, S. T. andLebleu, B., eds., Antisense Research and Applications, CRC Press, BocaRaton, 1993, pp. 276-278) and are aspects of base substitutions.

Modified nucleobases can comprise other synthetic and naturalnucleobases, such as 5-methylcytosine (5-me-C), 5-hydroxymethylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and otheralkyl derivatives of adenine and guanine, 2-propyl and other alkylderivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil andcytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudo-uracil),4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl andother 8-substituted adenines and guanines, 5-halo particularly 5-bromo,5-trifluoromethyl and other 5-substituted uracils and cytosines,7-methylquanine and 7-methyladenine, 8-azaguanine and 8-azaadenine,7-deazaguanine and 7-deazaadenine, and 3-deazaguanine and3-deazaadenine.

Complexes of a Genome-Targeting Nucleic Acid and a Endonuclease

A gRNA interacts with an endonuclease (e.g., a RNA-guided nuclease suchas Cas9), thereby forming a complex. The gRNA guides the endonuclease toa target polynucleotide.

The endonuclease and gRNA can each be administered separately to a cellor a subject. In some embodiments, the endonuclease can be pre-complexedwith one or more guide RNAs, or one or more crRNA together with atracrRNA. The pre-complexed material can then be administered to a cellor a subject. Such pre-complexed material is known as aribonucleoprotein particle (RNP). The endonuclease in the RNP can be,for example, a Cas9 endonuclease or a Cpf1 endonuclease. Theendonuclease can be flanked at the N-terminus, the C-terminus, or boththe N-terminus and C-terminus by one or more nuclear localizationsignals (NLSs). For example, a Cas9 endonuclease can be flanked by twoNLSs, one NLS located at the N-terminus and the second NLS located atthe C-terminus. The NLS can be any NLS known in the art, such as a SV40NLS. The molar ratio of genome-targeting nucleic acid to endonuclease inthe RNP can range from about 1:1 to about 10:1. For example, the molarratio of sgRNA to Cas9 endonuclease in the RNP can be 3:1.

Nucleic Acids Encoding System Components

The present disclosure provides a nucleic acid comprising a nucleotidesequence encoding a genome-targeting nucleic acid of the disclosure, anendonuclease of the disclosure, and/or any nucleic acid or proteinaceousmolecule necessary to carry out the aspects of the methods of thedisclosure. The encoding nucleic acids can be RNA, DNA, or a combinationthereof.

The nucleic acid encoding a genome-targeting nucleic acid of thedisclosure, an endonuclease of the disclosure, and/or any nucleic acidor proteinaceous molecule necessary to carry out the aspects of themethods of the disclosure can comprise a vector (e.g., a recombinantexpression vector).

The term “vector” refers to a nucleic acid molecule capable oftransporting another nucleic acid to which it has been linked. One typeof vector is a “plasmid”, which refers to a circular double-stranded DNAloop into which additional nucleic acid segments can be ligated. Anothertype of vector is a viral vector, wherein additional nucleic acidsegments can be ligated into the viral genome. Certain vectors arecapable of autonomous replication in a host cell into which they areintroduced (e.g., bacterial vectors having a bacterial origin ofreplication and episomal mammalian vectors). Other vectors (e.g.,non-episomal mammalian vectors) are integrated into the genome of a hostcell upon introduction into the host cell, and thereby are replicatedalong with the host genome.

In some examples, vectors can be capable of directing the expression ofnucleic acids to which they are operatively linked. Such vectors arereferred to herein as “recombinant expression vectors”, or more simply“expression vectors”, which serve equivalent functions.

The term “operably linked” means that the nucleotide sequence ofinterest is linked to regulatory sequence(s) in a manner that allows forexpression of the nucleotide sequence. The term “regulatory sequence” isintended to include, for example, promoters, enhancers and otherexpression control elements (e.g., polyadenylation signals). Suchregulatory sequences are well known in the art and are described, forexample, in Goeddel; Gene Expression Technology: Methods in Enzymology,1990, 185, Academic Press, San Diego, Calif. Regulatory sequencesinclude those that direct constitutive expression of a nucleotidesequence in many types of host cells, and those that direct expressionof the nucleotide sequence only in certain host cells (e.g.,tissue-specific regulatory sequences). It will be appreciated by thoseskilled in the art that the design of the expression vector can dependon such factors as the choice of the target cell, the level ofexpression desired, and the like.

Expression vectors contemplated include, but are not limited to, viralvectors based on vaccinia virus, poliovirus, adenovirus,adeno-associated virus, SV40, herpes simplex virus, humanimmunodeficiency virus, retrovirus (e.g., Murine Leukemia Virus, spleennecrosis virus, and vectors derived from retroviruses such as RousSarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, a lentivirus,human immunodeficiency virus, myeloproliferative sarcoma virus, andmammary tumor virus) and other recombinant vectors. Other vectorscontemplated for eukaryotic target cells include, but are not limitedto, the vectors pXT1, pSG5, pSVK3, pBPV, pMSG, and pSVLSV40 (Pharmacia).Other vectors can be used so long as they are compatible with the hostcell.

In some examples, a vector can comprise one or more transcription and/ortranslation control elements. Depending on the host/vector systemutilized, any of a number of suitable transcription and translationcontrol elements, including constitutive and inducible promoters,transcription enhancer elements, transcription terminators, etc. can beused in the expression vector. The vector can be a self-inactivatingvector that either inactivates the viral sequences or the components ofthe CRISPR machinery or other elements.

Non-limiting examples of suitable eukaryotic promoters (i.e., promotersfunctional in a eukaryotic cell) include those from cytomegalovirus(CMV) immediate early, herpes simplex virus (HSV) thymidine kinase,early and late SV40, long terminal repeats (LTRs) from retrovirus, humanelongation factor-1 α promoter (EF1α), chicken beta-actin promoter(CBA), ubiquitin C promoter (UBC), a hybrid construct comprising thecytomegalovirus enhancer fused to the chicken beta-actin promoter (CAG),a hybrid construct comprising the cytomegalovirus enhancer fused to thepromoter, the first exon, and the first intron of chicken beta-actingene (CAG or CAGGS), murine stem cell virus promoter (MSCV),phosphoglycerate kinase-1 locus promoter (PGK), and mousemetallothionein-I promoter.

A promoter can be an inducible promoter (e.g., a heat shock promoter,tetracycline-regulated promoter, steroid-regulated promoter,metal-regulated promoter, estrogen receptor-regulated promoter, etc.).The promoter can be a constitutive promoter (e.g., CMV promoter, UBCpromoter, CAG promoter). In some cases, the promoter can be a spatiallyrestricted and/or temporally restricted promoter (e.g., a tissuespecific promoter, a cell type specific promoter, etc.).

Introduction of the complexes, polypeptides, and nucleic acids of thedisclosure into cells can occur by viral or bacteriophage infection,transfection, conjugation, protoplast fusion, lipofection,electroporation, nucleofection, calcium phosphate precipitation,polyethyleneimine (PEI)-mediated transfection, DEAE-dextran mediatedtransfection, liposome-mediated transfection, particle gun technology,calcium phosphate precipitation, direct micro-injection,nanoparticle-mediated nucleic acid delivery, and the like.

III. Strategies to Evade Immune Response and Increase Survival

Described herein are strategies to enable genetically modified cells,i.e., universal donor cells, to increase their survival or viabilityand/or evade immune response following engraftment into a subject. Insome embodiments, these strategies enable universal donor cells tosurvive and/or evade immune response at higher success rates than anunmodified cell. In some embodiments, genetically modified cellscomprise the introduction of at least one genetic modification within ornear at least one gene that encodes a survival factor, wherein thegenetic modification comprises an insertion of a polynucleotide encodinga tolerogenic factor. The universal donor cells may further comprise atleast one genetic modification within or near a gene that encodes one ormore MHC-I or MHC-II human leukocyte antigens or a component or atranscriptional regulator of a MHC-I or MHC-II complex, wherein saidgenetic modification comprises an insertion of a polynucleotide encodinga second tolerogenic factor.

In some embodiments, genetically modified cells comprise theintroduction of at least one genetic modification within or near atleast one gene that decreases the expression of one or more MHC-I andMHC-II human leukocyte antigens relative to an unmodified cell; at leastone genetic modification that increases the expression of at least onepolynucleotide that encodes a tolerogenic factor relative to anunmodified cell; and at least one genetic modification that alters theexpression of at least one gene that encodes a survival factor relativeto an unmodified cell. In other embodiments, genetically modified cellscomprise at least one deletion or insertion-deletion mutation within ornear at least one gene that alters the expression of one or more MHC-Iand MHC-II human leukocyte antigens relative to an unmodified cell; andat least one insertion of a polynucleotide that encodes at least onetolerogenic factor at a site that partially overlaps, completelyoverlaps, or is contained within, the site of a deletion of a gene thatalters the expression of one or more MHC-I and MHC-II HLAs. In yet otherembodiments, genetically modified cells comprise at least one geneticmodification that alters the expression of at least one gene thatencodes a survival factor relative to an unmodified cell.

The genes that encode the major histocompatibility complex (MHC) arelocated on human Chr. 6p21. The resultant proteins coded by the MHCgenes are a series of surface proteins that are essential in donorcompatibility during cellular transplantation. MHC genes are dividedinto MHC class I (MHC-I) and MHC class II (MHC-II). MHC-I genes (HLA-A,HLA-B, and HLA-C) are expressed in almost all tissue cell types,presenting “non-self” antigen-processed peptides to CD8+ T cells,thereby promoting their activation to cytolytic CD8+ T cells.Transplanted or engrafted cells expressing “non-self” MHC-I moleculeswill cause a robust cellular immune response directed at these cells andultimately resulting in their demise by activated cytolytic CD8+ Tcells. MHC-I proteins are intimately associated withbeta-2-microglobulin (B2M) in the endoplasmic reticulum, which isessential for forming functional MHC-I molecules on the cell surface. Inaddition, there are three non-classical MHC-Ib molecules (HLA-E, HLA-F,and HLA-G), which have immune regulatory functions. MHC-II biomoleculeinclude HLA-DP, HLA-DM, HLA-DOA, HLA-DOB, HLA-DQ, and HLA-DR. Due totheir primary function in the immune response, MHC-I and MHC-IIbiomolecules contribute to immune rejection following cellularengraftment of non-host cells, e.g., cellular engraftment for purposesof regenerative medicine.

MHC-I cell surface molecules are composed of MHC-encoded heavy chains(HLA-A, HLA-B, or HLA-C) and the invariant subunit beta-2-microglobulin(B2M). Thus, a reduction in the concentration of B2M within a cellallows for an effective method of reducing the cell surface expressionof MHC-I cell surface molecules.

In some embodiments, a cell comprises a genomic modification of one ormore MHC-I or MHC-II genes. In some embodiments, a cell comprises agenomic modification of one or more polynucleotide sequences thatregulates the expression of MHC-I and/or MHC-II. In some embodiments, agenetic modification of the disclosure is performed using any geneediting method including but not limited to those methods describedherein.

In some embodiments, decreasing the expression of one or more MHC-I andMHC-II human leukocyte antigens relative to an unmodified cell isaccomplished by targeting, e.g., for genetic deletion and/or insertionof at least one base pair, in a MHC-I and/or MHC-II gene directly. Insome embodiments, decreasing the expression of one or more MHC-I andMHC-II human leukocyte antigens relative to an unmodified cell isaccomplished by targeting, e.g., for genetic deletion, a CIITA gene. Insome embodiments, decreasing the expression of one or more MHC-I andMHC-II human leukocyte antigens relative to an unmodified cell isaccomplished by targeting, e.g., for genetic deletion, at least onetranscriptional regulator of MHC-I or MHC-II. In some embodiments, atranscriptional regulator of MHC-I or MHC-II is a NLRC5, or CIITA gene.In some embodiments, a transcriptional regulator of MHC-I or MHC-II is aRFX5, RFXAP, RFXANK, NFY-A, NFY-B, NFY-C, IRF-1, and/or TAP1 gene.

In some embodiments, the genome of a cell has been modified to deletethe entirety or a portion of a HLA-A, HLA-B, and/or HLA-C gene. In someembodiments, the genome of a cell has been modified to delete theentirety or a portion of a promoter region of a HLA-A, HLA-B, and/orHLA-C gene. In some embodiments, the genome of a cell has been modifiedto delete the entirety or a portion of a gene that encodes atranscriptional regulator of MHC-I or MHC-II. In some embodiments, thegenome of a cell has been modified to delete the entirety or a portionof a promoter region of a gene that encodes a transcriptional regulatorof MHC-I or MHC-II.

In some embodiments, the genome of a cell has been modified to decreasethe expression of beta-2-microglobulin (B2M). B2M is a non-polymorphicgene that encodes a common protein subunit required for surfaceexpression of all polymorphic MHC class I heavy chains. HLA-I proteinsare intimately associated with B2M in the endoplasmic reticulum, whichis essential for forming functional, cell-surface expressed HLA-Imolecules. In some embodiments, the gRNA targets a site within the B2Mgene comprising a 5′-GCTACTCTCTCTTTCTGGCC-3′ sequence (SEQ ID NO: 1). Insome embodiments, the gRNA targets a site within the B2M gene comprisinga 5′-GGCCGAGATGTCTCGCTCCG-3′ sequence (SEQ ID NO: 2). In someembodiments, the gRNA targets a site within the B2M gene comprising a5′-CGCGAGCACAGCTAAGGCCA-3′ sequence (SEQ ID NO: 3). In alternateembodiments, the gRNA targets a site within the B2M gene comprising anyof the following sequences: 5′-TATAAGTGGAGGCGTCGCGC-3′ (SEQ ID NO: 35),5′-GAGTAGCGCGAGCACAGCTA-3′ (SEQ ID NO: 36), 5′-ACTGGACGCGTCGCGCTGGC-3′(SEQ ID NO: 37), 5′-AAGTGGAGGCGTCGCGCTGG-3′ (SEQ ID NO: 38),5-GGCCACGGAGCGAGACATCT-3′ (SEQ ID NO: 39), 5′-GCCCGAATGCTGTCAGCTTC-3′(SEQ ID NO: 40). 5′-CTCGCGCTACTCTCTCTTTC-3′ (SEQ ID NO: 41),5′-TCCTGAAGCTGACAGCATTC-3′ (SEQ ID NO: 42), 5′-TTCCTGAAGCTGACAGCATT-3′(SEQ ID NO: 43), or 5′-ACTCTCTCTTTCTGGCCTGG-3′ (SEQ ID NO: 44). In someembodiments, the gRNA comprises a polynucleotide sequence of any one ofSEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 35, SEQ ID NO: 36,SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO:41, SEQ ID NO: 42, SEQ ID NO: 43, or SEQ ID NO: 44. The gRNA/CRISPRnuclease complex targets and cleaves a target site in the B2M locus.Repair of a double-stranded break by NHEJ can result in a deletion of atleast on nucleotide and/or an insertion of at least one nucleotide,thereby disrupting or eliminating expression of B2M. Alternatively, theB2M locus can be targeted by at least two CRISPR systems each comprisinga different gRNA, such that cleavage at two sites in the B2M locus leadsto a deletion of the sequence between the two cuts, thereby eliminatingexpression of B2M.

In some embodiments, the genome of a cell has been modified to decreasethe expression of thioredoxin interacting protein (TXNIP). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-GAAGCGTGTCTTCATAGCGC-3′ sequence (SEQ ID NO: 15). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-TTACTCGTGTCAAAGCCGTT-3′ sequence (SEQ ID NO: 16). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-TGTCAAAGCCGTTAGGATCC-3′ sequence (SEQ ID NO: 17). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-GCCGTTAGGATCCTGGCTTG-3′ sequence (SEQ ID NO: 18). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-GCGGAGTGGCTAAAGTGCTT-3′ sequence (SEQ ID NO: 19). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-TCCGCAAGCCAGGATCCTAA-3′ sequence (SEQ ID NO: 20). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-GTTCGGCTTTGAGCTTCCTC-3′ sequence (SEQ ID NO: 21). In someembodiments, the gRNA targets site within the TXNIP gene comprising a5′-GAGATGGTGATCATGAGACC-3′ sequence (SEQ ID NO: 22). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-TTGTACTCATATTTGTTTCC-3′ sequence (SEQ ID NO: 23). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-AACAAATATGAGTACAAGTT-3′ sequence (SEQ ID NO: 24). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-GAAGCGTGTCTTCATAGCGCAGG-3′ sequence (SEQ ID NO: 45). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-TTACTCGTGTCAAAGCCGTTAGG-3′ sequence (SEQ ID NO: 46). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-TGTCAAAGCCGTTAGGATCCTGG-3′ sequence (SEQ ID NO: 47). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-GCCGTTAGGATCCTGGCTTGCGG-3′ sequence (SEQ ID NO: 48). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-GCGGAGTGGCTAAAGTGCTTTGG-3′ sequence (SEQ ID NO: 49). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-TCCGCAAGCCAGGATCCTAACGG-3′ sequence (SEQ ID NO: 50). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-GTTCGGCTTTGAGCTTCCTCAGG-3′ sequence (SEQ ID NO: 51). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-GAGATGGTGATCATGAGACCTGG-3′ sequence (SEQ ID NO: 52). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-TTGTACTCATATTTGTTTCCAGG-3′ sequence (SEQ ID NO: 53). In someembodiments, the gRNA targets a site within the TXNIP gene comprising a5′-AACAAATATGAGTACAAGTTCGG-3′ sequence (SEQ ID NO: 54). In someembodiments, the gRNA targets a target site within the TXNIP gene thatcomprises a polynucleotide sequence of any one of SEQ ID NO: 15-24 or45-54. In some embodiments, the gRNA targets a polynucleotide sequenceof any one of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO:18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ IDNO: 23, or SEQ ID NO: 24. The gRNA/CRISPR nuclease complex targets andcleaves a target site in the TXNIP gene locus. Repair of adouble-stranded break by NHEJ can result in a deletion of at least onnucleotide and/or an insertion of at least one nucleotide, therebydisrupting or eliminating expression of TXNIP. Alternatively, insertionof a polynucleotide encoding an exogenous gene into the TXNIP gene locuscan disrupt or eliminate expression of TXNIP.

In some embodiments, the genome of a cell has been modified to decreasethe expression of Class II transactivator (CIITA). CIITA is a member ofthe LR or nucleotide binding domain (NBD) leucine-rich repeat (LRR)family of proteins and regulates the transcription of MHC-II byassociating with the MHC enhanceosome. The expression of CIITA isinduced in B cells and dendritic cells as a function of developmentalstage and is inducible by IFN-γ in most cell types.

In some embodiments, the genome of a cell has been modified to decreasethe expression of the NLR family, CARD domain containing 5 (NLRC5).NLRC5 is a critical regulator of MHC-I-mediated immune responses and,similar to CIITA, NLRC5 is highly inducible by IFN-γ and can translocateinto the nucleus. NLRC5 activates the promoters of MHC-I genes andinduces the transcription of MHC-I as well as related genes involved inMHC-I antigen presentation.

In some embodiments, tolerogenic factors can be inserted or reinsertedinto genetically modified cells to create immune-privileged universaldonor cells. In some embodiments, the universal donor cells disclosedherein have been further modified to express one or more tolerogenicfactors. Exemplary tolerogenic factors include, without limitation, oneor more of HLA-C, HLA-E, HLA-F, HLA-G, PD-L1, CTLA-4-Ig, CD47,CI-inhibitor, and IL-35. In some embodiments, the genetic modification,e.g., insertion, of at least one polynucleotide encoding at least onetolerogenic factor enables a universal donor cell to inhibit or evadeimmune rejection with rates at least 1.05, at least 1.1, at least 1.25,at least 1.5, at least 2, at least 3, at least 4, at least 5, at least10, at least 20, or at least 50 times higher than an unmodified cellfollowing engraftment. In some embodiments, an insertion of apolynucleotide that encodes HLA-E, HLA-G, CTLA-4, CD47, and/or PD-L1enables a universal donor cell to inhibit or evade immune rejectionafter transplantation or engraftment into a host subject.

The polynucleotide encoding the tolerogenic factor generally comprisesleft and right homology arms that flank the sequence encoding thetolerogenic factor. The homology arms have substantial sequence homologyto genomic DNA at or near the targeted insertion site. For example, theleft homology arm can be a nucleotide sequence homologous with a regionlocated to the left or upstream of the target site or cut site, and theright homology arm can be a nucleotide sequence homologous with a regionlocated to the right or downstream of the target site or cut site. Theproximal end of each homology arm can be homologous to genomic DNAsequence abutting the cut site. Alternatively, the proximal end of eachhomology arm can be homologous to genomic DNA sequence located up toabout 10, 20, 30, 40, 50, 60, or 70 nucleobases away from the cut site.As such, the polynucleotide encoding the tolerogenic factor can beinserted into the targeted gene locus within about 10, 20, 30, 40, 50,60, or 70 base pairs of the cut site, and additional genomic DNAbordering the cut site (and having no homology to a homolog arm) can bedeleted. The homology arms can range in length from about 50 nucleotidesto several of thousands of nucleotides. In some embodiments, thehomology arms can range in length from about 500 nucleotides to about1000 nucleotides. The substantial sequence homology between the homologyarms and the genomic DNA can be at least about 80%, at least about 85%,at least about 90%, at least about 95%, or at least about 99%.

In some embodiments, the homology arms are used with B2M guides (e.g.,gRNAs comprising a nucleotide sequence of SEQ ID NO: 1-3, 35-44). Insome embodiments, the homology arms are designed to be used with any B2Mguide that would eliminate the start site of the B2M gene. In someembodiments, the B2M homology arms can comprise or consist essentiallyof a polynucleotide sequence of SEQ ID NO: 7 or 13, or a polynucleotidesequence having at least 85%, 90%, 95%, or 99% sequence identity withthat of SEQ ID NO: 7 or 13. In some embodiments, the left B2M homologyarm can comprise or consist essentially of SEQ ID NO: 7, or apolynucleotide sequence having at least 85%, 90%, 95%, or 99% sequenceidentity with that of SEQ ID NO: 7. In some embodiments, the right B2Mhomology arm can comprise or consist essentially of SEQ ID NO: 13, or apolynucleotide sequence having at least 85%, 90%, 95%, or 99% sequenceidentity with that of SEQ ID NO: 13.

In some embodiments, the homology arms are used with TXNIP guides (e.g.,gRNAs comprising a nucleotide sequence of SEQ ID NO: 15-24). In someembodiments, the homology arms are designed to be used with any TXNIPguide that targets exon 1 of TXNIP (e.g., gRNAs comprising a nucleotidesequence of SEQ ID NO: 15-20). In some embodiments, the TXNIP homologyarms can comprise or consist essentially of a polynucleotide sequence ofSEQ ID NO: 25 or 32, or a polynucleotide sequence having at least 85%,90%, 95%, or 99% sequence identity with that of SEQ ID NO: 25 or 32. Insome embodiments, the left TXNIP homology arm can comprise or consistessentially of SEQ ID NO: 25, or a polynucleotide sequence having atleast 85%, 90%, 95%, or 99% sequence identity with that of SEQ ID NO:25. In some embodiments, the right TXNIP homology arm can comprise orconsist essentially of SEQ ID NO: 32, or a polynucleotide sequencehaving at least 85%, 90%, 95%, or 99% sequence identity with that of SEQID NO: 32.

The at least one polynucleotide encoding at least one tolerogenic factorcan be operably linked to an exogenous promoter. The exogenous promotercan be a constitutive, inducible, temporal-, tissue-, or celltype-specific promoter. In some embodiments, the exogenous promoter is aCMV, EFla, PGK, CAG, or UBC promoter.

In some embodiments, the at least one polynucleotide encoding at leastone tolerogenic factor is inserted into a safe harbor locus, e.g., theAAVS 1 locus. In some embodiments, the at least one polynucleotideencoding at least one tolerogenic factor is inserted into a site orregion of genomic DNA that partially overlaps, completely overlaps, oris contained within (i.e., is within or near) a MHC-I gene, MHC-II gene,or a transcriptional regulator of MHC-I or MHC-II.

In some embodiments, a polynucleotide encoding PD-L1 is inserted at asite within or near a B2M gene locus. In some embodiments, apolynucleotide encoding PD-L1 is inserted at a site within or near a B2Mgene locus concurrent with, or following a deletion of all or part of aB2M gene or promoter. The polynucleotide encoding PD-L1 is operablylinked to an exogenous promoter. The exogenous promoter can be a CMVpromoter. In some embodiments, the polynucleotide comprises a nucleotidesequence of SEQ ID NO: 11.

In some embodiments, a polynucleotide encoding HLA-E is inserted at asite within or near a B2M gene locus. In some embodiments, apolynucleotide encoding HLA-E is inserted at a site within or near a B2Mgene locus concurrent with, or following a deletion of all or part of aB2M gene or promoter. The polynucleotide encoding HLA-E is operablylinked to an exogenous promoter. The exogenous promoter can be a CMVpromoter. In some embodiments, the polynucleotide comprises a nucleotidesequence of SEQ ID NO: 26, 27, 28, 29, 30, and/or 30. In someembodiments, the polynucleotide comprises a nucleotide sequence of SEQID NO: 55.

In some embodiments, a polynucleotide encoding HLA-G is inserted at asite within or near a HLA-A, HLA-B, or HLA-C gene locus. In someembodiments, a polynucleotide encoding HLA-G is inserted at a sitewithin or near a HLA-A, HLA-B, or HLA-C gene locus concurrent with, orfollowing a deletion of a HLA-A, HLA-B, or HLA-C gene or promoter.

In some embodiments, a polynucleotide encoding CD47 is inserted at asite within or near a CIITA gene locus. In some embodiments, apolynucleotide encoding CD47 is inserted at a site within or near aCIITA gene locus concurrent with, or following a deletion of a CIITAgene or promoter.

In some embodiments, a polynucleotide encoding HLA-G is inserted at asite within or near a HLA-A, HLA-B, or HLA-C gene locus concurrent withinsertion of a polynucleotide encoding CD47 at a site within or near aCIITA gene locus.

In some embodiments, the at least one polynucleotide encoding at leastone tolerogenic factor can be delivered to the cells as part of avector. For example, the vector may be a plasmid vector. In variousembodiments, the amount of plasmid vector delivered to the cells mayrange from about 0.5 μg to about 10 μg (per about 10⁶ cells). In someembodiments, the amount of plasmid may range from about 1 μg to about 8μg, from about 2 μg to about 6 μg, or from about 3 μg to about 5 μg. Inspecific embodiments, the amount of plasmid delivered to the cells maybe about 4 μg.

In some embodiments, a cell comprises increased or decreased expressionof one or more survival factors. In some embodiments, a cell comprisesan insertion of one or more polynucleotide sequences that encodes asurvival factor. In some embodiments, a cell comprises a deletion of oneof more survival factors. In some embodiments, a genetic modification ofthe disclosure is performed using any gene editing method including butnot limited to those methods described herein. In some embodiments, acell comprises increased or decreased expression of at least onesurvival factor relative to an unmodified cell. In some embodiments, asurvival factor is a member or a critical pathway involved in cellsurvival, e.g., hypoxia, reactive oxygen species, nutrient deprivation,and/or oxidative stress. In some embodiments, the genetic modificationof at least one survival factor enables a universal donor cell tosurvive for a longer time period, e.g., at least 1.05, at least 1.1, atleast 1.25, at least 1.5, at least 2, at least 3, at least 4, at least5, at least 10, at least 20, or at least 50 times longer time period,than an unmodified cell following engraftment. In some embodiments, asurvival factor is ZNF143, TXNIP, FOXO1, JNK, or MANF.

In some embodiments, a cell comprises an insertion of a polynucleotidethat encodes MANF enables a universal donor cell to survive aftertransplantation or engraftment into a host subject at higher survivalrates relative to an unmodified cell. In some embodiments, apolynucleotide that encodes MANF is inserted into a safe harbor locus.In some embodiments, a polynucleotide that encodes MANF is inserted intoa gene belonging to a MHC-I, MHC-II, or transcriptional regulator ofMHC-I or MHC-II.

In some embodiments, the genome of a cell has been modified to deletethe entirety or a portion of a ZNF143, TXNIP, FOXO1, and/or INK gene. Insome embodiments, the genome of a cell has been modified to delete theentirety or a portion of a promoter region of a ZNF143, TXNIP, FOXO1,and/or JNK gene.

In some embodiments, more than one survival factor is geneticallymodified within a cell.

In certain embodiments, cells having no MHC-II expression and moderateexpression of MHC-I are genetically modified to have no surfaceexpression of MHC-I or MHC-II. In another embodiment, cells with nosurface expression of MHC-I/II are further edited to have expression ofPD-L1, e.g., insertion of a polynucleotide encoding PD-L1. In yetanother embodiment, cells with no surface expression of MHC-I/II arefurther edited to have expression of PD-L1, e.g., insertion of apolynucleotide encoding PD-L1, and are also genetically modified toincrease or decrease the expression of at least one gene that encodes asurvival factor relative to an unmodified cell.

In some embodiments, the cells further comprise increased or decreasedexpression, e.g., by a genetic modification, of one or more additionalgenes that are not necessarily implicated in either immune evasion orcell survival post-engraftment. In some embodiments, the cells furthercomprise increased expression of one or more safety switch proteinsrelative to an unmodified cell. In some embodiments, the cells compriseincreased expression of one or more additional genes that encode asafety switch protein. In some embodiments, a safety switch is also asuicide gene. In some embodiments, a safety switch is herpes simplexvirus-1 thymidine kinase (HSV-tk) or inducible caspase-9. In someembodiments, a polynucleotide that encodes at least one safety switch isinserted into a genome, e.g., into a safe harbor locus. In some otherembodiments, the one or more additional genes that are geneticallymodified encode one or more of safety switch proteins; targetingmodalities; receptors; signaling molecules; transcription factors;pharmaceutically active proteins or peptides; drug target candidates;and proteins promoting engraftment, trafficking, homing, viability,self-renewal, persistence, and/or survival thereof integrated with theconstruct.

One aspect of the present invention provides a method of generatinggenome-engineered universal donor cells, wherein a universal donor cellcomprises at least one targeted genomic modification at one or moreselected sites in genome, the method comprising genetically engineeringa cell type as described herein by introducing into said cells one ormore construct of to allow targeted modification at selected site;introducing into said cells one or more double strand breaks at theselected sites using one or more endonuclease capable of selected siterecognition; and culturing the edited cells to allow endogenous DNArepair to generate targeted insertions or deletions at the selectedsites; thereby obtaining genome-modified universal donor cells. Thegenome-modified universal donor cells can undergo successive rounds ofgenome modification such that multiple sites are targeted and modified.The genome-modified cells are cultured, characterized, selected, andexpanded using techniques well known in the art. The universal donorcells generated by this method will comprise at least one functionaltargeted genomic modification, and wherein the genome-modified cells, ifthey are stem cells, are then capable of being differentiated intoprogenitor cells or fully-differentiated cells.

In some other embodiments, the genome-engineered universal donor cellscomprise introduced or increased expression in at least one of HLA-E,HLA-G, CD47, or PD-L1. In some embodiments, the genome-engineereduniversal donor cells are HLA class I and/or class II deficient. In someembodiment, the genome-engineered universal donor cells comprise B2Mnull or low. In some embodiments, the genome-engineered universal donorcells comprise integrated or non-integrated exogenous polynucleotideencoding one or more of HLA-E, HLA-G, and PD-L1 proteins. In someembodiments, said introduced expression is an increased expression fromeither non-expressed or lowly expressed genes comprised in said cells.In some embodiments, the non-integrated exogenous polynucleotides areintroduced using Sendai virus, AAV, episomal, or plasmid. In someembodiment, the universal donor cells are B2M null, with introducedexpression of one or more of HLA-E, HLA-G, PD-L1, and increased ordecreased expression of at least one safety switch protein. In anotherembodiment, the universal donor cells are HLA-A, HLA-B, and HLA-C null,with introduced expression of one or more of HLA-E, HLA-G, PD-L1, and atleast one safety switch protein. In some embodiment, the universal donorcells are B2M null, with introduced expression of one or more of HLA-E,HLA-G PD-L1, and increased or decreased expression of at least onesurvival factor, e.g., MANF. Methods of generating any of thegenetically modified cells described herein are contemplated to beperformed using at least any of the gene editing methods describedherein.

IV. Cell Types

Cells as described herein, e.g., universal donor cells (andcorresponding unmodified cells) may belong to any possible class of celltype. In some embodiments, a cell, e.g., universal donor cell (andcorresponding unmodified cell) may be a mammalian cell. In someembodiments, a cell, e.g., universal donor cell (and correspondingunmodified cell) may be a human cell. In some embodiments, a cell, e.g.,universal donor cell (and corresponding unmodified cell) may be a stemcell. In some embodiments, a cell, e.g., universal donor cell (andcorresponding unmodified cell) may be a pluripotent stem cell (PSC). Insome embodiments, a cell, e.g., a universal donor cell (andcorresponding unmodified cell) may be an embryonic stem cell (ESC), anadult stem cell (ASC), an induced pluripotent stem cell (iPSC), or ahematopoietic stem or progenitor cell (HSPC) (also called ahematopoietic stem cell (HSC)). In some embodiments, a cell, e.g.,universal donor cell (and corresponding unmodified cell) may be adifferentiated cell. In some embodiments, a cell, e.g., universal donorcell (and corresponding unmodified cell) may be a somatic cell, e.g., animmune system cell or a contractile cell, e.g., a skeletal muscle cell.

The cells, e.g., universal donor stem cells, described herein may bedifferentiated into relevant cell types to assess HLA expression, aswell as the evaluation of immunogenicity of the universal stem celllines. In general, differentiation comprises maintaining the cells ofinterest for a period time and under conditions sufficient for the cellsto differentiate into the differentiated cells of interest. For example,the universal stem cells disclosed herein may be differentiated intomesenchymal progenitor cells (MPCs), hypoimmunogenic cardiomyocytes,muscle progenitor cells, blast cells, endothelial cells (ECs),macrophages, hepatocytes, beta cells (e.g., pancreatic beta cells),pancreatic endoderm progenitors, pancreatic endocrine progenitors,hematopoietic progenitor cells, or neural progenitor cells (NPCs). Insome embodiments, the universal donor cell may be differentiated intodefinitive endoderm cells, primitive gut tube cells, posterior foregutcells, pancreatic endoderm cells (PEC), pancreatic endocrine cells,immature beta cells, or maturing beta cells.

Stem cells are capable of both proliferation and giving rise to moreprogenitor cells, these in turn having the ability to generate a largenumber of mother cells that can in turn give rise to differentiated ordifferentiable daughter cells. The daughter cells themselves can beinduced to proliferate and produce progeny that subsequentlydifferentiate into one or more mature cell types, while also retainingone or more cells with parental developmental potential. The term “stemcell” refers then, to a cell with the capacity or potential, underparticular circumstances, to differentiate to a more specialized ordifferentiated phenotype, and which retains the capacity, under certaincircumstances, to proliferate without substantially differentiating. Inone aspect, the term progenitor or stem cell refers to a generalizedmother cell whose descendants (progeny) specialize, often in differentdirections, by differentiation, e.g., by acquiring completely individualcharacters, as occurs in progressive diversification of embryonic cellsand tissues. Cellular differentiation is a complex process typicallyoccurring through many cell divisions. A differentiated cell may derivefrom a multipotent cell that itself is derived from a multipotent cell,and so on. While each of these multipotent cells may be considered stemcells, the range of cell types that each can give rise to may varyconsiderably. Some differentiated cells also have the capacity to giverise to cells of greater developmental potential. Such capacity may benatural or may be induced artificially upon treatment with variousfactors. In many biological instances, stem cells can also be“multipotent” because they can produce progeny of more than one distinctcell type, but this is not required for “stem-ness.”

A “differentiated cell” is a cell that has progressed further down thedevelopmental pathway than the cell to which it is being compared. Thus,stem cells can differentiate into lineage-restricted precursor cells(such as a myocyte progenitor cell), which in turn can differentiateinto other types of precursor cells further down the pathway (such as amyocyte precursor), and then to an end-stage differentiated cell, suchas a myocyte, which plays a characteristic role in a certain tissuetype, and may or may not retain the capacity to proliferate further. Insome embodiments, the differentiated cell may be a pancreatic beta cell.

Embryonic Stem Cells

The cells described herein may be embryonic stem cells (ESCs). ESCs arederived from blastocytes of mammalian embryos and are able differentiateinto any cell type and propagate rapidly. ESCs are also believed to havea normal karyotype, maintaining high telomerase activity, and exhibitingremarkable long-term proliferative potential, making these cellsexcellent candidates for use as universal donor cells.

Adult Stem Cells

The cells described herein may be adult stem cells (ASCs). ASCs areundifferentiated cells that may be found in mammals, e.g., humans. ASCsare defined by their ability to self-renew, e.g., be passaged throughseveral rounds of cell replication while maintaining theirundifferentiated state, and ability to differentiate into severaldistinct cell types, e.g., glial cells. Adult stem cells are a broadclass of stem cells that may encompass hematopoietic stem cells, mammarystem cells, intestinal stem cells, mesenchymal stem cells, endothelialstem cells, neural stem cells, olfactory adult stem cells, neural creststem cells, and testicular cells.

Induced Pluripotent Stem Cells

The cells described herein may be induced pluripotent stem cells(iPSCs). An iPSC may be generated directly from an adult human cell byintroducing genes that encode critical transcription factors involved inpluripotency, e.g., OCT4, SOX2, cMYC, and KLF4. An iPSC may be derivedfrom the same subject to which subsequent progenitor cells are to beadministered. That is, a somatic cell can be obtained from a subject,reprogrammed to an induced pluripotent stem cell, and thenre-differentiated into a progenitor cell to be administered to thesubject (e.g., autologous cells). However, in the case of autologouscells, a risk of immune response and poor viability post-engraftmentremain.

Human Hematopoietic Stem and Progenitor Cells

The cells described herein may be human hematopoietic stem andprogenitor cells (hHSPCs). This stem cell lineage gives rise to allblood cell types, including erythroid (erythrocytes or red blood cells(RBCs)), myeloid (monocytes and macrophages, neutrophils, basophils,eosinophils, megakaryocytes/platelets, and dendritic cells), andlymphoid (T-cells, B-cells, NK-cells). Blood cells are produced by theproliferation and differentiation of a very small population ofpluripotent hematopoietic stem cells (HSCs) that also have the abilityto replenish themselves by self-renewal. During differentiation, theprogeny of HSCs progress through various intermediate maturationalstages, generating multi-potential and lineage-committed progenitorcells prior to reaching maturity. Bone marrow (BM) is the major site ofhematopoiesis in humans and, under normal conditions, only small numbersof hematopoietic stem and progenitor cells (HSPCs) can be found in theperipheral blood (PB). Treatment with cytokines, some myelosuppressivedrugs used in cancer treatment, and compounds that disrupt theinteraction between hematopoietic and BM stromal cells can rapidlymobilize large numbers of stem and progenitors into the circulation.

Differentiation of Cells into Other Cell Types

Another step of the methods of the present disclosure may comprisedifferentiating cells into differentiated cells. The differentiatingstep may be performed according to any method known in the art. Forexample, human iPSCs are differentiated into definitive endoderm usingvarious treatments, including activin and B27 supplement (LifeTechnologies). The definitive endoderm is further differentiated intohepatocyte, the treatment includes: FGF4, HGF, BMP2, BMP4, Oncostatin M,Dexamethasone, etc. (Duan et al, Stem Cells, 2010; 28:674-686; Ma et al,Stem Cells Translational Medicine, 2013; 2:409-419). In anotherembodiment, the differentiating step may be performed according toSawitza et al, Sci Rep. 2015; 5:13320. A differentiated cell may be anysomatic cell of a mammal, e.g., a human. In some embodiments, a somaticcell may be an exocrine secretory epithelial cells (e.g., salivary glandmucous cell, prostate gland cell), a hormone-secreting cell (e.g.,anterior pituitary cell, gut tract cell, pancreatic islet), akeratinizing epithelial cell (e.g., epidermal keratinocyte), a wetstratified barrier epithelial cell, a sensory transducer cell (e.g., aphotoreceptor), an autonomic neuron cells, a sense organ and peripheralneuron supporting cell (e.g., Schwann cell), a central nervous systemneuron, a glial cell (e.g., astrocyte, oligodendrocyte), a lens cell, anadipocyte, a kidney cell, a barrier function cell (e.g., a duct cell),an extracellular matrix cell, a contractile cell (e.g., skeletal musclecell, heart muscle cell, smooth muscle cell), a blood cell (e.g.,erythrocyte), an immune system cell (e.g., megakaryocyte, microglialcell, neutrophil, Mast cell, a T cell, a B cell, a Natural Killer cell),a germ cell (e.g., spermatid), a nurse cell, or an interstitial cell.

In general, populations of the universal donor cells disclosed hereinmaintain expression of the inserted one or more nucleotide sequencesover time. For example, at least about 50%, at least about 55%, at leastabout 60%, at least about 65%, at least about 70%, at least about 75%,at least about 80%, at least about 85%, at least about 90%, at leastabout 95%, or at least about 99% of the universal donor cells expressthe one or more tolerogenic factors. Moreover, populations oflineage-restricted or fully differentiated cells derived from theuniverisal donor cells disclosed herein maintain expression of theinserted one or more nucleotide sequences over time. For example, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 95%, or at leastabout 99% of the lineage-restricted or fully differentiated cellsexpress the one or more tolerogenic factors.

V. Formulations and Administrations

Formulation and Delivery for Gene Editing

Guide RNAs, polynucleotides, e.g., polynucleotides that encode atolerogenic factor or polynucleotides that encode an endonuclease, andendonucleases as described herein may be formulated and delivered tocells in any manner known in the art.

Guide RNAs and/or polynucleotides may be formulated withpharmaceutically acceptable excipients such as carriers, solvents,stabilizers, adjuvants, diluents, etc., depending upon the particularmode of administration and dosage form. Guide RNAs and/orpolynucleotides compositions can be formulated to achieve aphysiologically compatible pH, and range from a pH of about 3 to a pH ofabout 11, about pH 3 to about pH 7, depending on the formulation androute of administration. In some cases, the pH can be adjusted to arange from about pH 5.0 to about pH 8. In some cases, the compositionscan comprise a therapeutically effective amount of at least one compoundas described herein, together with one or more pharmaceuticallyacceptable excipients. Optionally, the compositions can comprise acombination of the compounds described herein, or can include a secondactive ingredient useful in the treatment or prevention of bacterialgrowth (for example and without limitation, anti-bacterial oranti-microbial agents), or can include a combination of reagents of thepresent disclosure.

Suitable excipients include, for example, carrier molecules that includelarge, slowly metabolized macromolecules such as proteins,polysaccharides, polylactic acids, polyglycolic acids, polymeric aminoacids, amino acid copolymers, and inactive virus particles. Otherexemplary excipients can include antioxidants (for example and withoutlimitation, ascorbic acid), chelating agents (for example and withoutlimitation, EDTA), carbohydrates (for example and without limitation,dextrin, hydroxyalkylcellulose, and hydroxyalkylmethylcellulose),stearic acid, liquids (for example and without limitation, oils, water,saline, glycerol and ethanol), wetting or emulsifying agents, pHbuffering substances, and the like.

Guide RNA polynucleotides (RNA or DNA) and/or endonucleasepolynucleotide(s) (RNA or DNA) can be delivered by viral or non-viraldelivery vehicles known in the art. Alternatively, endonucleasepolypeptide(s) can be delivered by viral or non-viral delivery vehiclesknown in the art, such as electroporation or lipid nanoparticles. Infurther alternative aspects, the DNA endonuclease can be delivered asone or more polypeptides, either alone or pre-complexed with one or moreguide RNAs, or one or more crRNA together with a tracrRNA.

Polynucleotides can be delivered by non-viral delivery vehiclesincluding, but not limited to, nanoparticles, liposomes,ribonucleoproteins, positively charged peptides, small moleculeRNA-conjugates, aptamer-RNA chimeras, and RNA-fusion protein complexes.Some exemplary non-viral delivery vehicles are described in Peer andLieberman, Gene Therapy, 2011, 18: 1127-1133 (which focuses on non-viraldelivery vehicles for siRNA that are also useful for delivery of otherpolynucleotides).

For polynucleotides of the disclosure, the formulation may be selectedfrom any of those taught, for example, in International ApplicationPCT/US2012/069610.

Polynucleotides, such as guide RNA, sgRNA, and mRNA encoding anendonuclease, may be delivered to a cell or a subject by a lipidnanoparticle (LNP).

A LNP refers to any particle having a diameter of less than 1000 nm, 500nm, 250 nm, 200 nm, 150 nm, 100 nm, 75 nm, 50 nm, or 25 nm.Alternatively, a nanoparticle may range in size from 1-1000 nm, 1-500nm, 1-250 nm, 25-200 nm, 25-100 nm, 35-75 nm, or 25-60 nm.

LNPs may be made from cationic, anionic, or neutral lipids. Neutrallipids, such as the fusogenic phospholipid DOPE or the membranecomponent cholesterol, may be included in LNPs as ‘helper lipids’ toenhance transfection activity and nanoparticle stability. Limitations ofcationic lipids include low efficacy owing to poor stability and rapidclearance, as well as the generation of inflammatory oranti-inflammatory responses.

LNPs may also be comprised of hydrophobic lipids, hydrophilic lipids, orboth hydrophobic and hydrophilic lipids.

Any lipid or combination of lipids that are known in the art can be usedto produce a LNP. Examples of lipids used to produce LNPs are: DOTMA,DOSPA, DOTAP, DMRIE, DC-cholesterol, DOTAP-cholesterol,GAP-DMORIE-DPyPE, and GL67A-DOPE-DMPE-polyethylene glycol (PEG).Examples of cationic lipids are: 98N12-5, C12-200, DLin-KC2-DMA (KC2),DLin-MC3-DMA (MC3), XTC, MD1, and 7C1. Examples of neutral lipids are:DPSC, DPPC, POPC, DOPE, and SM. Examples of PEG-modified lipids are:PEG-DMG, PEG-CerC14, and PEG-CerC20.

The lipids can be combined in any number of molar ratios to produce aLNP. In addition, the polynucleotide(s) can be combined with lipid(s) ina wide range of molar ratios to produce a LNP.

A recombinant adeno-associated virus (AAV) vector can be used fordelivery. Techniques to produce rAAV particles, in which an AAV genometo be packaged that includes the polynucleotide to be delivered, rep andcap genes, and helper virus functions are provided to a cell arestandard in the art. Production of rAAV typically requires that thefollowing components are present within a single cell (denoted herein asa packaging cell): a rAAV genome, AAV rep and cap genes separate from(i.e., not in) the rAAV genome, and helper virus functions. The AAV repand cap genes may be from any AAV serotype for which recombinant viruscan be derived, and may be from a different AAV serotype than the rAAVgenome ITRs, including, but not limited to, AAV serotypes describedherein. Production of pseudotyped rAAV is disclosed in, for example,international patent application publication number WO 01/83692.

Formulation and Administration of Cells, e.g., Universal Donor Cells

Genetically modified cells, e.g., universal donor cells, as describedherein may be formulated and administered to a subject by any mannerknown in the art.

The terms “administering,” “introducing”, “implanting”, “engrafting” and“transplanting” are used interchangeably in the context of the placementof cells, e.g., progenitor cells, into a subject, by a method or routethat results in at least partial localization of the introduced cells ata desired site. The cells e.g., progenitor cells, or theirdifferentiated progeny can be administered by any appropriate route thatresults in delivery to a desired location in the subject where at leasta portion of the implanted cells or components of the cells remainviable. The period of viability of the cells after administration to asubject can be as short as a few hours, e.g., twenty-four hours, to afew days, to as long as several years, or even the life time of thesubject, i.e., long-term engraftment.

A genetically modified cell, e.g., universal donor cell, as describedherein may be viable after administration to a subject for a period thatis longer than that of an unmodified cell.

In some embodiments, a composition comprising cells as described hereinmay be administered by a suitable route, which may include intravenousadministration, e.g., as a bolus or by continuous infusion over a periodof time. In some embodiments, intravenous administration may beperformed by intramuscular, intraperitoneal, intracerebrospinal,subcutaneous, intra-articular, intrasynovial, or intrathecal routes. Insome embodiments, a composition may be in solid form, aqueous form, or aliquid form. In some embodiments, an aqueous or liquid form may benebulized or lyophilized. In some embodiments, a nebulized orlyophilized form may be reconstituted with an aqueous or liquidsolution.

A cell composition can also be emulsified or presented as a liposomecomposition, provided that the emulsification procedure does notadversely affect cell viability. The cells and any other activeingredient can be mixed with excipients that are pharmaceuticallyacceptable and compatible with the active ingredient, and in amountssuitable for use in the therapeutic methods described herein.

Additional agents included in a cell composition can includepharmaceutically acceptable salts of the components therein.Pharmaceutically acceptable salts include the acid addition salts(formed with the free amino groups of the polypeptide) that are formedwith inorganic acids, such as, for example, hydrochloric or phosphoricacids, or such organic acids as acetic, tartaric, mandelic and the like.Salts formed with the free carboxyl groups can also be derived frominorganic bases, such as, for example, sodium, potassium, ammonium,calcium or ferric hydroxides, and such organic bases as isopropylamine,trimethylamine, 2-ethylamino ethanol, histidine, procaine and the like.

Physiologically tolerable carriers are well known in the art. Exemplaryliquid carriers are sterile aqueous solutions that contain no materialsin addition to the active ingredients and water, or contain a buffersuch as sodium phosphate at physiological pH value, physiological salineor both, such as phosphate-buffered saline. Still further, aqueouscarriers can contain more than one buffer salt, as well as salts such assodium and potassium chlorides, dextrose, polyethylene glycol and othersolutes. Liquid compositions can also contain liquid phases in additionto and to the exclusion of water. Exemplary of such additional liquidphases are glycerin, vegetable oils such as cottonseed oil, andwater-oil emulsions. The amount of an active compound used in the cellcompositions that is effective in the treatment of a particular disorderor condition can depend on the nature of the disorder or condition, andcan be determined by standard clinical techniques.

In some embodiments, a composition comprising cells may be administeredto a subject, e.g., a human subject, who has, is suspected of having, oris at risk for a disease. In some embodiments, a composition may beadministered to a subject who does not have, is not suspected of havingor is not at risk for a disease. In some embodiments, a subject is ahealthy human. In some embodiments, a subject e.g., a human subject, whohas, is suspected of having, or is at risk for a genetically inheritabledisease. In some embodiments, the subject is suffering or is at risk ofdeveloping symptoms indicative of a disease. In some embodiments, thedisease is diabetes, e.g., type I diabetes or type II diabetes.

VI. Specific Compositions and Methods of the Disclosure

Accordingly, the present disclosure relates in particular to thefollowing non-limiting compositions and methods.

In a first composition, Composition 1, the present disclosure provides acomposition comprising a universal donor cell comprising a nucleotidesequence encoding a first tolerogenic factor inserted within or near agene encoding a survival factor, wherein the universal donor cellexpresses the tolerogenic factor and has disrupted expression of thesurvival factor, and the universal donor cell has increased immuneevasion and/or cell survival compared to a control cell.

In another composition, Composition 2, the present disclosure provides acomposition, as provided in Composition 1, wherein the control cell is awild type cell or a cell that does not comprise the inserted nucleotidesequence.

In another composition, Composition 3, the present disclosure provides acomposition, as provided in Compositions 1 or 2, wherein the disruptedexpression of the survival factor comprises reduced or eliminatedexpression.

In another composition, Composition 4, the present disclosure provides acomposition, as provided in any one of Compositions 1 to 3, wherein thefirst tolerogenic factor is PD-L1, HLA-E, HLA-G, CTLA-4, or CD47.

In another composition, Composition 5, the present disclosure provides acomposition, as provided in any one of Compositions 1 to 4, wherein thesurvival factor is TXNIP, ZNF143, FOXO1, JNK, or MANF.

In another composition, Composition 6, the present disclosure provides acomposition, as provided in any one of Compositions claims 1 to 5,wherein the first tolerogenic factor is HLA-E and the survival factor isTXNIP.

In another composition, Composition 7, the present disclosure provides acomposition, as provided in Compositions 5 or 6, wherein the nucleotidesequence encoding HLA-E comprises sequence encoding a HLA-E trimercomprising a B2M signal peptide fused to an HLA-G presentation peptidefused to a B2M membrane protein fused to HLA-E without its signalpeptide.

In another composition, Composition 8, the present disclosure provides acomposition, as provided in Composition 7, wherein the sequence encodingthe HLA-E trimer consists essentially of SEQ ID NO: 55.

In another composition, Composition 9, the present disclosure provides acomposition, as provided in any one of Compositions 1 to 8, wherein thenucleotide sequence encoding the first tolerogenic factor is operablylinked to an exogenous promoter,

In another composition, Composition 10, the present disclosure providesa composition, as provided in Composition 9, wherein the exogenouspromoter is a CMV, EF1α, PGK, CAG, or UBC promoter.

In another composition, Composition 11, the present disclosure providesa composition, as provided in any one of Compositions claims 1 to 10,further comprising a nucleotide sequence encoding a second tolerogenicfactor inserted within or near a gene encoding a MHC-I or MHC-II humanleukocyte antigen or a component or a transcriptional regulator of aMHC-I or MHC-II complex, wherein the universal donor cell expresses thetolerogenic factor and has disrupted expression of the MHC-I or MHC-IIhuman leukocyte antigen or the component or the transcriptionalregulator of the MHC-I or MHC-II complex.

In another composition, Composition 12, the present disclosure providesa composition, as provided in Composition 11, wherein the disruptedexpression of the MHC-I or MHC-II human leukocyte antigen or thecomponent or the transcriptional regulator of the MHC-I or MHC-IIcomplex comprises reduced or eliminated expression.

In another composition, Composition 13, the present disclosure providesa composition, as provided in Compositions 11 or 12, wherein the secondtolerogenic factor is PD-L1, HLA-E, HLA-G, CTLA-4, or CD47.

In another composition, Composition 14, the present disclosure providesa composition, as provided in any one of Compositions 11 to 13, whereinthe MHC-I or MHC-II human leukocyte antigen or the component or thetranscriptional regulator of the MHC-I or MHC-II complex is HLA-A,HLA-B, HLA-C, HLA-DP, HLA-DM, HLA-DOA, HLA-DOB, HLA-DQ, HLA-DR, B2M,NLRC5, CIITA, RFX5, RFXAP, or RFXANK

In another composition, Composition 15, the present disclosure providesa composition, as provided in any one of Compositions 11 to 14, whereinthe second tolerogenic factor is PD-L1 and the MHC-I or MHC-II humanleukocyte antigen or the component or the transcriptional regulator ofthe MHC-I or MHC-II complex is B2M.

In another composition, Composition 16, the present disclosure providesa composition, as provided in Composition 15, wherein the nucleotidesequence encoding PD-L1 consists essentially of SEQ ID NO: 11.

In another composition, Composition 17, the present disclosure providesa composition, as provided in any one of Compositions 11 to 16, whereinthe nucleotide sequence encoding the second tolerogenic factor isoperably linked to an exogenous promoter,

In another composition, Composition 18, the present disclosure providesa composition, as provided in Composition 17, wherein the exogenouspromoter is a CMV, EF1α, PGK, CAG, or UBC promoter.

In another composition, Composition 19, the present disclosure providesa composition, as provided in any one of Compositions 11 to 18, whereinthe first tolerogenic factor is HLA-E, the survival factor is TXNIP, thesecond tolerogenic factor is PD-L1, and the MHC-I or MHC-II humanleukocyte antigen or the component or the transcriptional regulator ofthe MHC-I or MHC-II complex is B2M.

In another composition, Composition 20, the present disclosure providesa composition, as provided in any one of Compositions 1 to 19, whereinthe cell is a stem cell.

In another composition, Composition 21, the present disclosure providesa composition, as provided in Composition 20, wherein the stem cell isan embryonic stem cell, an adult stem cell, an induced pluripotent stemcell, or a hematopoietic stem cell.

In another composition, Composition 22, the present disclosure providesa composition, as provided in any one of Compositions 1 to 19, whereinthe cell is a differentiated cell or a somatic cell.

In another composition, Composition 23, the present disclosure providesa composition, as provided in any one of Compositions 1 to 19, whereinthe cell is capable of being differentiated into lineage-restrictedprogenitor cells or fully differentiated somatic cells.

In another composition, Composition 24, the present disclosure providesa composition, as provided in Composition 23, wherein thelineage-restricted progenitor cells are pancreatic endoderm progenitors,pancreatic endocrine progenitors, mesenchymal progenitor cells, muscleprogenitor cells, blast cells, hematopoietic progenitor cells, or neuralprogenitor cells.

In another composition, Composition 25, the present disclosure providesa composition, as provided in Composition 23, wherein the fullydifferentiated somatic cells are pancreatic beta cells, epithelialcells, endodermal cells, macrophages, hepatocytes, adipocytes, kidneycells, blood cells, cardiomyocytes, or immune system cells.

In another composition, Composition 26, the present disclosure providesa composition, as provided in any one of Compositions 1 to 25, whereinthe composition comprises a plurality of universal donor cells.

In another composition, Composition 27, the present disclosure providesa composition, as provided in Composition 26, wherein the compositioncomprised a population of lineage-restricted progenitor cells or fullydifferentiated somatic cells derived from the plurality of universaldonor cells.

In another composition, Composition 28, the present disclosure providesa composition, as provided in Composition 27, wherein thelineage-restricted progenitor cells are pancreatic endoderm progenitors,pancreatic endocrine progenitors, mesenchymal progenitor cells, muscleprogenitor cells, blast cells, hematopoietic progenitor cells, or neuralprogenitor cells, and the fully differentiated somatic cells arepancreatic beta cells, epithelial cells, endodermal cells, macrophages,hepatocytes, adipocytes, kidney cells, blood cells, cardiomyocytes, orimmune system cells.

In another composition, Composition 29, the present disclosure providesa composition, as provided in Compositions 6 or 19, wherein thecomposition comprises a plurality of universal donor cells.

In another composition, Composition 30, the present disclosure providesa composition, as provided in Composition 29, wherein the compositioncomprised a population of lineage-restricted progenitor cells or fullydifferentiated somatic cells derived from the plurality of universaldonor cells.

In another composition, Composition 31, the present disclosure providesa composition, as provided in Composition 30, wherein thelineage-restricted progenitor cells are definitive endoderm cells,primitive gut tube cells, posterior foregut cells, pancreatic endodermprogenitors, pancreatic endocrine progenitors, immature beta cells, ormaturing beta cells, and the fully differentiated somatic cells arepancreatic beta cells.

In another composition, Composition 32, the present disclosure providesa composition, as provided in Composition 26 or 29, wherein at leastabout 50%, at least about 70%, or at least about 90% of the cellsexpress the first tolerogenic factor, the second tolerogenic factor, orthe first and second tolerogenic factors.

In another composition, Composition 33, the present disclosure providesa composition, as provided in any one of Compositions 27, 28, 30, or 31,wherein at least about 50%, at least about 70%, or at least about 90% ofthe cells express the first tolerogenic factor, the second tolerogenicfactor, or the first and second tolerogenic factors.

In another composition, Composition 34, the present disclosure providesa composition comprising the plurality of cells of Composition 26 or thepopulation of cells of Compositions 27 or 28.

In another composition, Composition 35, the present disclosure providesa composition, as provided in Composition 34 for use in treating asubject in need thereof.

In another composition, Composition 36, the present disclosure providesa composition, as provided in Composition 35, wherein the subject has,is suspected of having, or is at risk for a disease.

In another composition, Composition 37, the present disclosure providesa composition, as provided in Composition 36, wherein the disease is agenetically inheritable disease.

In another composition, Composition 38, the present disclosure providesa composition comprising the plurality of cells of Composition 29 or thepopulation of cells of Compositions 30 or 31.

In another composition, Composition 39, the present disclosure providesa composition, as provided in Composition 38 for treating diabetes in asubject in need thereof.

In another composition, Composition 40, the present disclosure providesa composition, as provided in Composition 39, wherein the subject hastype I diabetes or type II diabetes.

In another composition, Composition 41, the present disclosure providesa composition, as provided in any one of Compositions 35 to 40, whereinthe subject is human.

In a first method, Method 1, the present disclosure provides a method ofobtaining cells for administration to a subject in need thereof, themethod comprising: (a) obtaining or having obtained the plurality ofuniversal donor cells of any one of Composition 26, 29, or 32, and (b)maintaining the plurality of universal donor cells for a time and underconditions sufficient for the cells to differentiate intolineage-restricted progenitor cells or fully differentiated somaticcells.

In another method, Method 2, the present disclosure provides a methodfor treating of a subject in need thereof, the method comprising: (a)obtaining or having obtained the plurality of universal donor cells ofany one of Compositions 26, 29, or 32 following differentiation intolineage-restricted progenitor cells or fully differentiated somaticcells; and (b) administering the lineage-restricted progenitor cells orfully differentiated somatic cells to the subject.

In another method, Method 3, the present disclosure provides a method asprovided in Method 2, wherein administering comprises implanting adevice comprising the lineage-restricted progenitor cells or fullydifferentiated somatic cells into the subject.

In another method, Method 4, the present disclosure provides a method asprovided in of any one of Methods 1 to 3, wherein the lineage-restrictedprogenitor cells are pancreatic endoderm progenitors, pancreaticendocrine progenitors, mesenchymal progenitor cells, muscle progenitorcells, blast cells, hematopoietic progenitor cells, or neural progenitorcells, and the fully differentiated somatic cells are pancreatic betacells, epithelial cells, endodermal cells, macrophages, hepatocytes,adipocytes, kidney cells, blood cells, cardiomyocytes, or immune systemcells.

In another method, Method 5, the present disclosure provides a method asprovided in of any one of Methods 1 to 4, wherein the subject has, issuspected of having, or is at risk for a disease.

In another method, Method 6, the present disclosure provides a method asprovided in Method 5, wherein the disease is a genetically inheritabledisease.

In another method, Method 7, the present disclosure provides a method asprovided in of any one of Methods 1 to 6, wherein the subject is human.

In another method, Method 8, the present disclosure provides a methodfor treating diabetes in a subject in need thereof, the methodcomprising: (a) obtaining or having obtained the plurality of universaldonor cells of Composition 29 or 32 following differentiation intopancreatic endoderm cells, pancreatic endocrine cells, immature betacells, maturing beta cell, or pancreatic beta cells; and (b)administering the pancreatic endoderm cells, pancreatic endocrine cells,immature beta cells, maturing beta cells, or pancreatic beta cells tothe subject.

In another method, Method 9, the present disclosure provides a method asprovided in Method 8, wherein administering comprises implanting adevice comprising the pancreatic endoderm cells, pancreatic endocrinecells, immature beta cells, maturing beta cell, or pancreatic beta cellsinto the subject.

In another method, Method 10, the present disclosure provides a methodas provided in Method 8 or 9, wherein the subject has type I diabetes ortype II diabetes.

In another method, Method 11, the present disclosure provides a methodas provided in any one of Methods 8 to 10, wherein the subject is human.

In another composition, Composition 41, the present disclosure providesa composition comprising a universal donor cell comprising a nucleotidesequence encoding HLA class I histocompatibility antigen, alpha chain E(HLA-E) inserted within or near a gene encoding thioredoxin interactingprotein (TXNIP), wherein the universal donor cell expresses HLA-E andhas disrupted expression of TXNIP, and the universal donor cell hasincreased immune evasion and/or cell survival compared to a control.

In another composition, Composition 42, the present disclosure providesa composition, as provided in Composition 41, wherein the control cellis a wild type cell or a cell that does not comprise the insertednucleotide sequence.

In another composition, Composition 43, the present disclosure providesa composition, as provided in Composition 41, wherein the disruptedexpression of TXNIP comprises reduced or eliminated expression.

In another composition, Composition 44, the present disclosure providesa composition, as provided in Composition 41, wherein the nucleotidesequence encoding HLA-E comprises a sequence encoding a HLA-E trimercomprising a B2M signal peptide fused to an HLA-G presentation peptidefused to a B2M membrane protein fused to HLA-E without its signalpeptide.

In another composition, Composition 45, the present disclosure providesa composition, as provided in Composition 44, wherein the sequenceencoding the HLA-E trimer consists essentially of SEQ ID NO: 55.

In another composition, Composition 46, the present disclosure providesa composition, as provided in Composition 41, wherein the nucleotidesequence encoding HLA-E is operably linked to an exogenous promoter,

In another composition, Composition 47, the present disclosure providesa composition, as provided in Composition 41, wherein the exogenouspromoter is a CAG promoter.

In another composition, Composition 48, the present disclosure providesa composition, as provided in Composition 41, wherein the cell is a stemcell.

In another composition, Composition 49, the present disclosure providesa composition, as provided in Composition 48, wherein the stem cell isan embryonic stem cell, an adult stem cell, an induced pluripotent stemcell, or a hematopoietic stem cell.

In another composition, Composition 50, the present disclosure providesa composition, as provided in Composition 41, wherein the cell is adifferentiated cell or a somatic cell.

In another composition, Composition 51, the present disclosure providesa composition, as provided in Composition 41, wherein the cell iscapable of being differentiated into lineage-restricted progenitor cellsor fully differentiated somatic cells.

In another composition, Composition 52, the present disclosure providesa composition, as provided in Composition 51, wherein thelineage-restricted progenitor cells are definitive endoderm cells,primitive gut tube cells, posterior foregut cells, pancreatic endodermprogenitors, pancreatic endocrine progenitors, immature beta cells, ormaturing beta cells, and the fully differentiated somatic cells arepancreatic beta cells.

In another composition, Composition 53, the present disclosure providesa composition comprising a plurality of universal donor cells asprovided in Composition 41.

In another composition, Composition 54, the present disclosure providesa composition, as provided in Composition 53, wherein at least about 50%of the cells express HLA-E.

In another composition, Composition 55, the present disclosure providesa composition, as provided in Composition 53, wherein at least about 70%of the cells express HLA-E.

In another composition, Composition 56, the present disclosure providesa composition, as provided in Composition 53, wherein at least about 90%of the cells express HLA-E.

In another composition, Composition 57, the present disclosure providesa composition comprising a population of lineage-restricted progenitorcells or fully differentiated somatic cells derived from the pluralityof universal donor cells of Composition 53.

In another composition, Composition 58, the present disclosure providesa composition, as provided in Composition 57, wherein thelineage-restricted progenitor cells are definitive endoderm cells,primitive gut tube cells, posterior foregut cells, pancreatic endodermprogenitors, pancreatic endocrine progenitors, immature beta cells, ormaturing beta cells, and the fully differentiated somatic cells arepancreatic beta cells.

In another composition, Composition 59, the present disclosure providesa composition, as provided in Composition 58, wherein at least about 50%of the cells express HLA-E.

In another composition, Composition 60, the present disclosure providesa composition, as provided in Composition 59, wherein at least about 70%of the cells express HLA-E.

In another composition, Composition 61, the present disclosure providesa composition, as provided in Composition 59, wherein at least about 90%of the cells express HLA-E.

In another composition, Composition 62, the present disclosure providesa composition comprising a genetically modified cell having introducedor increased expression of HLA class I histocompatibility antigen, alphachain E (HLA-E) and disrupted expression of thioredoxin interactingprotein (TXNIP), wherein the genetically modified cell has increasedimmune evasion and/or cell survival compared to an unmodified cell.

In another composition, Composition 63, the present disclosure providesa composition, as provided in Composition 62, which comprises anucleotide sequence encoding HLA-E inserted within or near a geneencoding TXNIP, thereby disrupting the TXNIP gene.

In another composition, Composition 64, the present disclosure providesa composition, as provided in Composition 62, wherein the disruptedexpression of TXNIP comprises reduced or eliminated expression

In another method, Method 12, the present disclosure provides a methodfor treating diabetes in a subject in need thereof, the methodcomprising: obtaining or having obtained the plurality of universaldonor cells of Composition 53 following differentiation into pancreaticendoderm cells, pancreatic endocrine cells, immature beta cells,maturing beta cells, or pancreatic beta cells; and (b) administering thepancreatic endoderm cells, pancreatic endocrine cells, immature betacells, maturing beta cell, or pancreatic beta cells to the subject.

In another method, Method 13, the present disclosure provides a method,as provided in Method 12, wherein administering comprises implanting adevice comprising the pancreatic endoderm cells, pancreatic endocrinecells, immature beta cells, maturing beta cells, or pancreatic betacells into the subject.

In another method, Method 14, the present disclosure provides a method,as provided in Method 12, wherein the subject has type I diabetes ortype II diabetes.

In another method, Method 15, the present disclosure provides a method,as provided in Method 12, wherein the subject is human.

In another composition, Composition 65, the present disclosure providesa composition comprising a universal donor cell comprising (a) anucleotide sequence encoding programmed death-ligand 1 (PD-L1) insertedwithin or near a gene encoding beta-2 microglobulin (B2M) and (b) anucleotide sequence encoding HLA class I histocompatibility antigen,alpha chain E (HLA-E) inserted within or near a gene encodingthioredoxin interacting protein (TXNIP), wherein the universal donorcell expresses PD-L1 and HLA-E and has disrupted expression of B2M andTXNIP, and the universal donor cell has increased immune evasion and/orcell survival compared to a control cell.

In another composition, Composition 66, the present disclosure providesa composition, as provided in Composition 65, wherein the control cellis a wild type cell or a cell that does not comprise the insertednucleotide sequence.

In another composition, Composition 67, the present disclosure providesa composition, as provided in Composition 65, wherein the disruptedexpression of B2M comprises reduced or eliminated expression of B2M andthe disrupted expression of TXNIP comprises reduced or eliminatedexpression of TXNIP.

In another composition, Composition 68, the present disclosure providesa composition, as provided in Composition 65, wherein the nucleotidesequence encoding PD-L1 consists essentially of SEQ ID NO: 11.

In another composition, Composition 69, the present disclosure providesa composition, as provided in Composition 65, wherein the nucleotidesequence encoding HLA-E comprises a sequence encoding a HLA-E trimercomprising a B2M signal peptide fused to an HLA-G presentation peptidefused to a B2M membrane protein fused to HLA-E without its signalpeptide.

In another composition, Composition 70, the present disclosure providesa composition, as provided in Composition 69, wherein the sequenceencoding the HLA-E trimer consists essentially of SEQ ID NO: 55.

In another composition, Composition 71, the present disclosure providesa composition, as provided in Composition 65, wherein the nucleotidesequence encoding PD-L1 is operably linked to an exogenous promoter, andthe nucleotide sequence encoding HLA-E is operably linked to anexogenous promoter.

In another composition, Composition 72, the present disclosure providesa composition, as provided in Composition 71, wherein the exogenouspromoter is a CAG promoter.

In another composition, Composition 73, the present disclosure providesa composition, as provided in Composition 65, wherein the cell is a stemcell.

In another composition, Composition 74, the present disclosure providesa composition, as provided in Composition 73, wherein the stem cell isan embryonic stem cell, an adult stem cell, an induced pluripotent stemcell, or a hematopoietic stem cell.

In another composition, Composition 75, the present disclosure providesa composition, as provided in Composition 65, wherein the cell is adifferentiated cell or a somatic cell.

In another composition, Composition 76, the present disclosure providesa composition, as provided in Composition 65, wherein the cell iscapable of being differentiated into lineage-restricted progenitor cellsor fully differentiated somatic cells.

In another composition, Composition 77, the present disclosure providesa composition, as provided in Composition 76, wherein thelineage-restricted progenitor cells are definitive endoderm cells,primitive gut tube cells, posterior foregut cells, pancreatic endodermprogenitors, pancreatic endocrine progenitors, immature beta cells, ormaturing beta cells, and the fully differentiated somatic cells arepancreatic beta cells.

In another composition, Composition 78, the present disclosure providesa composition comprising a plurality of universal donor cells asprovided in Composition 65.

In another composition, Composition 79, the present disclosure providesa composition, as provided in Composition 78, wherein at least about 50%of the cells express PD-L1 and/or at least about 50% of the cellsexpress HLA-E.

In another composition, Composition 80, the present disclosure providesa composition, as provided in Composition 78, wherein at least about 70%of the cells express PD-L1 and/or at least about 70% of the cellsexpress HLA-E.

In another composition, Composition 81, the present disclosure providesa composition, as provided in Composition 78, wherein at least about 90%of the cells express PD-L1 and/or at least about 90% of the cellsexpress HLA-E.

In another composition, Composition 82, the present disclosure providesa composition comprising a population of lineage-restricted progenitorcells or fully differentiated somatic cells derived from the pluralityof universal donor cells, as provided in Composition 78.

In another composition, Composition 83, the present disclosure providesa composition, as provided in Composition 82, wherein thelineage-restricted progenitor cells are definitive endoderm cells,primitive gut tube cells, posterior foregut cells, pancreatic endodermprogenitors, pancreatic endocrine progenitors, immature beta cells, ormaturing beta cells, and the fully differentiated somatic cells arepancreatic beta cells.

In another composition, Composition 84, the present disclosure providesa composition, as provided in Composition 83, wherein at least about 50%of the cells express PD-L1 and/or at least about 50% of the cellsexpress HLA-E.

In another composition, Composition 85, the present disclosure providesa composition, as provided in Composition 83, wherein at least about 70%of the cells express PD-L1 and/or at least about 70% of the cellsexpress HLA-E.

In another composition, Composition 86, the present disclosure providesa composition, as provided in Composition 83, wherein at least about 90%of the cells express PD-L1 and/or at least about 90% of the cellsexpress HLA-E.

In another composition, Composition 87, the present disclosure providesa composition comprising a genetically modified cell having introducedor increased expression of PD-L1 and HLA-E and disrupted expression ofB2M and TXNIP, wherein the genetically modified cell has increasedimmune evasion and/or cell survival compared to an unmodified cell.

In another composition, Composition 88, the present disclosure providesa composition, as provided in Composition 87, which comprises anucleotide sequence encoding PD-L1 inserted within or near a geneencoding B2M, thereby disrupting the B2M gene, and a nucleotide sequenceencoding HLA-E inserted within or near a gene encoding TXNIP, therebydisrupting the TXNIP gene.

In another composition, Composition 89, the present disclosure providesa composition, as provided in Composition 87, wherein disruptedexpression of B2M and TXNIP comprises reduced or eliminated expressionof B2M and TXNIP.

In another method, Method 16, the present disclosure provides a methodfor treating diabetes in a subject in need thereof, the methodcomprising: (a) obtaining or having obtained the plurality of universaldonor cells of Composition 78 following differentiation into pancreaticendoderm cells, pancreatic endocrine cells, immature beta cells,maturing beta cell, or pancreatic beta cells; and (b) administering thepancreatic endoderm cells, pancreatic endocrine cells, immature betacells, maturing beta cells, or pancreatic beta cells to the subject.

In another method, Method 17, the present disclosure provides a method,as provided in Method 16, wherein administering comprises implanting adevice comprising the pancreatic endoderm cells, pancreatic endocrinecells, immature beta cells, maturing beta cells, or pancreatic betacells into the subject.

In another method, Method 18, the present disclosure provides a method,as provided in Method 16, wherein the subject has type I diabetes ortype II diabetes.

In another method, Method 19, the present disclosure provides a method,as provided in Method 16, wherein the subject is human.

In another method, Method 20, the present disclosure provides a methodfor generating a universal donor cell, the method comprising deliveringto a cell: (a) a first site-directed nuclease targeting a site within ornear a gene that encodes a survival factor; and (b) a first nucleic acidcomprising a nucleotide sequence encoding a first tolerogenic factorthat is flanked by (i) a nucleotide sequence homologous with a regionlocated left of the target site of (a) and (ii) a nucleotide sequencehomologous with a region located right of the target site of (a),wherein the first site-directed nuclease cleaves the target site of (a)and the first nucleic acid of (b) is inserted at a site that partiallyoverlaps, completely overlaps, or is contained within, the site of (a),thereby generating a universal donor cell, wherein the universal donorcell has increased cell survival compared to a cell in which the nucleicacid of (b) has not been inserted.

In another method, Method 21, the present disclosure provides a method,as provided in Method 20, wherein the survival factor is TXNIP, ZNF143,FOXO1, JNK, or MANF.

In another method, Method 22, the present disclosure provides a method,as provided in Methods 20 or 21, wherein the first tolerogenic factor isPD-L1, HLA-E, HLA-G, CTLA-4, or CD47.

In another method, Method 23, the present disclosure provides a method,as provided in any one of Methods 20 to 22, wherein the survival factoris TXNIP.

In another method, Method 24, the present disclosure provides a method,as provided in Method 23, wherein the first tolerogenic factor is HLA-E.

In another method, Method 25, the present disclosure provides a method,as provided in any one of Methods 20 to 24, wherein the firstsite-directed nuclease is a CRISPR system comprising a CRISPR nucleaseand a guide RNA (gRNA).

In another method, Method 26, the present disclosure provides a method,as provided in any one of Methods 20 to 25, wherein the CRISPR nucleaseis a Type II Cas9 nuclease or a Type V Cfp1 nuclease, and the CRISPRnuclease is linked to at least one nuclear localization signal.

In another method, Method 27, the present disclosure provides a method,as provided in any one of Methods 20 to 26, wherein the gRNA comprises aspacer sequence corresponding to a target sequence consisting of SEQ IDNOS: 15-24.

In another method, Method 28, the present disclosure provides a method,as provided in any one of Methods 25 to 27, wherein the nucleotidesequence of (b)(i) consists essentially of SEQ ID NO: 25, and thenucleotide sequence of (b)(ii) consists essentially of SEQ ID NO: 32.

In another method, Method 29, the present disclosure provides a method,as provided in any one of Methods 20 to 28, wherein the method furthercomprises delivering to the cell: (c) a second site-directed nucleasetargeting a site within or near a gene that encodes one or more of aMHC-I or human leukocyte antigens or a component or a transcriptionalregulator of a MHC-I or MHC-II complex; and (d) a second nucleic acidcomprising a nucleotide sequence encoding a second tolerogenic factorthat is flanked by (iii) a nucleotide sequence homologous with a regionlocated left of the target site of (c) and a (iv) nucleotide sequencehomologous with a region located right of the target site of (c),wherein the second tolerogenic factor of (d) differs from the firsttolerogenic factor (b), wherein the second site-directed nucleasecleaves the target site of (c) and the second nucleic acid of (d) isinserted at a site that partially overlaps, completely overlaps, or iscontained within, the site of (c), wherein the universal donor cell hasincreased immune evasion and/or cell survival compared to a cell inwhich the second nucleic acid of (d) has not been inserted.

In another method, Method 30, the present disclosure provides a method,as provided in Method 29, wherein the MHC-I or MHC-II human leukocyteantigen or the component or the transcriptional regulator of the MHC-Ior MHC-II complex is HLA-A, HLA-B, HLA-C, HLA-DP, HLA-DM, HLA-DOA,HLA-DOB, HLA-DQ, HLA-DR, B2M, NLRC5, CIITA, RFX5, RFXAP, or RFXANK.

In another method, Method 31, the present disclosure provides a method,as provided in Methods 29 or 30, wherein the second tolerogenic factoris PD-L1, HLA-E, HLA-G, CTLA-4, or CD47.

In another method, Method 32, the present disclosure provides a method,as provided in any one of Methods 29 to 31, wherein the MHC-I or MHC-IIhuman leukocyte antigen or the component or the transcriptionalregulator of the MHC-I or MHC-II complex is B2M.

In another method, Method 33, the present disclosure provides a method,as provided in Method 32, wherein the second tolerogenic factor isPD-L1.

In another method, Method 34, the present disclosure provides a method,as provided in any one of Methods 29 to 33, wherein the secondsite-directed nuclease is CRISPR system comprising a CRISPR nuclease anda gRNA.

In another method, Method 35, the present disclosure provides a method,as provided in Method 34, wherein the CRISPR nuclease is a Type II Cas9nuclease or a Type V Cfp1 nuclease, and the CRISPR nuclease is linked toat least one nuclear localization signal.

In another method, Method 36, the present disclosure provides a method,as provided in Methods 34 or 35, wherein the gRNA comprises a spacersequence corresponding to a target sequence consisting of SEQ ID NOS:1-3 or 35-44.

In another method, Method 37, the present disclosure provides a method,as provided in any one of Methods 34 to 36, wherein the nucleotidesequence of (d)(iii) consists essentially of SEQ ID NO: 7, and thenucleotide sequence of (d)(iv) consists essentially of SEQ ID NO: 13.

In another method, Method 38, the present disclosure provides a method,as provided in any one of Methods 25 to 28 or 34 to 37, wherein theCRISPR nuclease and the gRNA are present at a molar ratio of 1:3.

In another method, Method 39, the present disclosure provides a method,as provided in any one of Methods 20 to 38, wherein the nucleotidesequence encoding the first tolerogenic factor is operably linked to anexogenous promoter, and the nucleotide sequence encoding the secondtolerogenic factor is operably linked to an exogenous promoter.

In another method, Method 40, the present disclosure provides a method,as provided in Method 39, wherein the exogenous promoter is aconstitutive, inducible, temporal-, tissue-, or cell type-specificpromoter, optionally wherein the exogenous promoter is a CMV, EF1α, PGK,CAG, or UBC promoter.

In another method, Method 41, the present disclosure provides a A methodfor generating a universal donor cell, the method comprising deliveringto a cell: (a) a first site-directed nuclease targeting a site within ornear a gene that encodes a survival factor; (b) a first nucleic acidcomprising a nucleotide sequence encoding a first tolerogenic factorthat is flanked by (i) a nucleotide sequence homologous with a regionlocated left of the target site of (a) and (ii) a nucleotide sequencehomologous with a region located right of the target site of (a),wherein the first site-directed nuclease cleaves the target site of (a)and, through a process of homologous recombination, the first nucleicacid of (b) is utilized as a template for inserting the nucleotidesequence encoding the first tolerogenic factor into a site thatpartially overlaps, completely overlaps, or is contained within, thesite of (a), thereby disrupting the gene of (a); (c) a secondsite-directed nuclease targeting a site within or near a gene thatencodes one or more of a MHC-I or MHC-II human leukocyte antigen or acomponent or a transcriptional regulator of a MHC-I or MHC-II complex;and (d) a second nucleic acid comprising a nucleotide sequence encodinga second tolerogenic factor that is flanked by (iii) a nucleotidesequence homologous with a region located left of the target site of (c)and a (iv) nucleotide sequence homologous with a region located right ofthe target site of (c), wherein the tolerogenic factor of (d) differsfrom the tolerogenic factor (b), wherein the second site-directednuclease cleaves the target site of (c) and, through a process ofhomologous recombination, the second nucleic acid of (d) is utilized asa template for inserting the nucleotide sequence encoding the secondtolerogenic factor into a site that partially overlaps, completelyoverlaps, or is contained within, the site of (c), thereby disruptingthe gene of (c), thereby generating a universal donor cell, wherein theuniversal donor cell has increased cell survival compared to a cell inwhich the first nucleic acid of (b) and the second nucleic acid of (d)has not been inserted.

In another method, Method 42, the present disclosure provides a method,as provided in Method 41, wherein the survival factor is TXNIP, thefirst tolerogenic factor is HLA-E, the MHC-I or MHC-II human leukocyteantigen or a component or a transcriptional regulator of a MHC-I orMHC-II complex is B2M, and the second tolerogenic factor is PD-L1.

In another method, Method 43, the present disclosure provides a method,as provided in any one of Methods 20 to 42, wherein the cell is amammalian cell, optionally wherein the cell is a human cell.

In another method, Method 44, the present disclosure provides a method,as provided in any one of Methods 20 to 43, wherein the cell is a stemcell.

In another method, Method 45, the present disclosure provides a method,as provided in any one of Methods 20 to 43, wherein the cell is apluripotent stem cell, an embryonic stem cell, an adult stem cell, aninduced pluripotent stem cell, or a hematopoietic stem cell.

In another method, Method 46, the present disclosure provides a method,as provided in any one of Methods 20 to 43, wherein the cell is adifferentiated cell, or a somatic cell.

In another method, Method 47, the present disclosure provides a method,as provided in any one of Methods 20 to 43, wherein the universal donorcell is capable of being differentiated into lineage-restrictedprogenitor cells or fully differentiated somatic cells.

In another method, Method 48, the present disclosure provides a method,as provided in Method 47, wherein the lineage-restricted progenitorcells are pancreatic endoderm progenitors, pancreatic endocrineprogenitors, mesenchymal progenitor cells, muscle progenitor cells,blast cells, hematopoietic progenitor cells, or neural progenitor cells.

In another method, Method 49, the present disclosure provides a method,as provided in Method 47, wherein the fully differentiated somatic cellsare endocrine secretory cells such as pancreatic beta cells, epithelialcells, endodermal cells, macrophages, hepatocytes, adipocytes, kidneycells, blood cells, or immune system cells.

In another method, Method 49A, the present disclosure provides a method,as provided in Method 47, wherein the fully differentiated somatic cellsare cardiomyocyte, or immune system cells.

In another composition, Composition 90, the present disclosure providesa composition comprising a plurality of universal donor cells generatedby any one of Methods 20 to 49.

In another composition, Composition 91, the present disclosure providesa composition, as provided by Composition 90, maintained for a time andunder conditions sufficient for the cells to undergo differentiation.

In another composition, Composition 92, the present disclosure providesa composition, as provided by Composition 90 or 91, for use in treatinga subject in need thereof.

In another composition, Composition 93, the present disclosure providesa composition, as provided by Composition 92, wherein the subject is ahuman who has, is suspected of having, or is at risk for a disease.

In another method, Method 50, the present disclosure provides a methodcomprising administering to a subject the plurality of universal donorcells of Compositions 90 or 91.

In another method, Method 51, the present disclosure provides a methodfor treating of a subject in need thereof, the method comprising: (a)obtaining or having obtained the plurality of universal donor cells ofComposition 90 following differentiation into lineage-restrictedprogenitor cells or fully differentiated somatic cells; and (b)administering the lineage-restricted progenitor cells or fullydifferentiated somatic cells to the subject.

In another method, Method 52, the present disclosure provides a methodof obtaining cells for administration to a subject in need thereof, themethod comprising: (a) obtaining or having obtained the universal donorcells of claim 31; and (b) maintaining the universal donor cells for atime and under conditions sufficient for the cells to differentiate intolineage-restricted progenitor cells or fully differentiated somaticcells.

In another method, Method 53, the present disclosure provides a method,as provided by Methods 51 or 52, wherein the lineage-restrictedprogenitor cells are pancreatic endoderm progenitors, pancreaticendocrine progenitors, mesenchymal progenitor cells, muscle progenitorcells, blast cells, hematopoietic progenitor cells, or neural progenitorcells.

In another method, Method 54, the present disclosure provides a method,as provided by Methods 51 or 52, wherein the fully differentiatedsomatic cells are endocrine secretory cells such as pancreatic betacells, epithelial cells, endodermal cells, macrophages, hepatocytes,adipocytes, kidney cells, blood cells, or immune system cells.

In another method, Method 54A, the present disclosure provides a method,as provided in Method 51 or 52, wherein the fully differentiated somaticcells are cardiomyocytes.

In another method, Method 55, the present disclosure provides a method,as provided by Methods 50 to 54, wherein the subject is a human who has,is suspected of having, or is at risk for a disease.

In another method, Method 56, the present disclosure provides a method,as provided by Method 55, wherein the disease is a geneticallyinheritable disease.

In another composition, Composition 93, the present disclosure providesa guide RNA comprising a spacer sequence corresponding to a targetsequence consisting of SEQ ID NO: 15-24.

In another method, Method 57, the present disclosure provides an invitro method for generating a universal donor cell, the methodcomprising delivering to a stem cell: (a) an RNA-guided nuclease; (b) aguide RNA (gRNA) targeting a target site in a thioredoxin interactingprotein (TXNIP) gene locus; and (c) a vector comprising a nucleic acid,the nucleic acid comprising: (i) a nucleotide sequence encoding atolerogenic factor; (ii) a nucleotide sequence consisting essentially ofSEQ ID NO: 25 and having sequence homology with a genomic region locatedleft and within 50 nucleobases of the target site; and (iii) anucleotide sequence consisting essentially of SEQ ID NO: 32 and havingsequence homology with a genomic region located right and within 50nucleobases of the target site, wherein (i) is flanked by (ii) and(iii); wherein the TXNIP gene locus is cleaved at the target site andthe nucleic acid is inserted into the TXNIP gene locus, therebydisrupting the TXNIP gene and generating a universal donor cell, whereinthe universal donor cell has increased immune evasion and/or cellsurvival compared to a control cell.

In another method, Method 57A, the present disclosure provides a method,as provided by Method 57, wherein the nucleic acid is inserted into theTXNIP gene locus within 50 base pairs of the target site.

In another method, Method 58, the present disclosure provides a method,as provided by Method 57, wherein the control cell is a wild type cellor a cell that does not comprise the inserted nucleic acid.

In another method, Method 59, the present disclosure provides a method,as provided by Method 57, wherein the disrupted TXNIP gene has reducedor eliminated expression of TXNIP.

In another method, Method 60, the present disclosure provides a method,as provided by Method 57, wherein the gRNA comprises a spacer sequencecorresponding to a sequence consisting of SEQ ID NO: 15-24.

In another method, Method 61, the present disclosure provides a method,as provided by Method 57, wherein the gRNA comprises a spacer sequencecorresponding to a sequence consisting of SEQ ID NO: 20.

In another method, Method 62, the present disclosure provides a method,as provided by Method 57, wherein the vector is a plasmid vector.

In another method, Method 63, the present disclosure provides a method,as provided by Method 57, wherein the tolerogenic factor is HLA class Ihistocompatibility antigen, alpha chain E (HLA-E).

In another method, Method 64, the present disclosure provides a method,as provided by Method 63, wherein the nucleotide sequence encoding HLA-Ecomprises a sequence encoding a HLA-E trimer comprising a B2M signalpeptide fused to an HLA-G presentation peptide fused to a B2M membraneprotein fused to HLA-E without its signal peptide.

In another method, Method 65, the present disclosure provides a method,as provided by Method 63, wherein the sequence encoding the HLA-E trimerconsists essentially of SEQ ID NO: 55.

In another method, Method 66, the present disclosure provides a method,as provided by Method 65, wherein the sequence encoding the HLA-E trimeris operably linked to an exogenous promoter.

In another method, Method 67, the present disclosure provides a method,as provided by Method 66, wherein the exogenous promoter is a CMV, EF1α,PGK, CAG, or UBC promoter.

In another method, Method 68, the present disclosure provides a method,as provided by Method 57, wherein the RNA-guided nuclease is a Cas9nuclease.

In another method, Method 69, the present disclosure provides a method,as provided by Method 68, wherein the Cas9 nuclease is linked to atleast one nuclear localization signal.

In another method, Method 70, the present disclosure provides a method,as provided by Method 69, wherein the Cas9 nuclease and the gRNA arepresent in a molar ratio of 1:3.

In another method, Method 71, the present disclosure provides a method,as provided by Method 57, wherein the stem cell is an embryonic stemcell, an adult stem cell, an induced pluripotent stem cell, or ahematopoietic stem cell.

In another method, Method 72, the present disclosure provides a method,as provided by Method 57, wherein the stem cell is a human stem cell.

In another method, Method 73, the present disclosure provides an invitro method for generating a universal donor cell, the methodcomprising delivering to a stem cell: (a) an RNA-guided nuclease; (b) aguide RNA (gRNA) targeting a target site in a thioredoxin interactingprotein (TXNIP) gene locus, and (c) a vector comprising a nucleic acid,the nucleic acid comprising: (i) a nucleotide sequence encoding atolerogenic factor; (ii) a nucleotide sequence having sequence homologywith a genomic region located left and within 50 nucleobases of thetarget site; and (iii) a nucleotide sequence having sequence homologywith a genomic region located right and within 50 nucleobases of thetarget site, wherein (i) is flanked by (ii) and (iii), and the vectorcomprises a nucleotide sequence consisting of SEQ ID NO: 34 or 56;wherein the TXNIP gene locus is cleaved at the target site and thenucleic acid is inserted into the TXNIP gene locus, thereby disruptingthe TXNIP gene and generating a universal donor cell, wherein theuniversal donor cell has increased immune evasion and/or cell survivalcompared to a control cell.

In another method, Method 73A, the present disclosure provides a method,as provided by Method 73, wherein the nucleic acid is inserted into theTXNIP gene locus within 50 base pairs of the target site.

In another method, Method 74, the present disclosure provides a method,as provided by Method 73, wherein the control cell is a wild type cellor a cell that does not comprise the inserted nucleic acid.

In another method, Method 75, the present disclosure provides a method,as provided by Method 73, wherein the disrupted TXNIP gene has reducedor eliminated expression of TXNIP.

In another method, Method 76, the present disclosure provides a method,as provided by Method 73, wherein the gRNA comprises a spacer sequencecorresponding to a sequence consisting of SEQ ID NO: 15-24.

In another method, Method 77, the present disclosure provides a method,as provided by Method 73, wherein the gRNA comprises a spacer sequencecorresponding to a sequence consisting of SEQ ID NO: 20.

In another method, Method 78, the present disclosure provides a method,as provided by Method 73, wherein the vector is a plasmid vector.

In another method, Method 79, the present disclosure provides a method,as provided by Method 73, wherein the tolerogenic factor is HLA class Ihistocompatibility antigen, alpha chain E (HLA-E).

In another method, Method 80, the present disclosure provides a method,as provided by Method 73, wherein the RNA-guided nuclease is a Cas9nuclease.

In another method, Method 81, the present disclosure provides a method,as provided by Method 80, wherein the Cas9 nuclease is linked to atleast one nuclear localization signal.

In another method, Method 82, the present disclosure provides a method,as provided by Method 80, wherein the Cas9 nuclease and the gRNA arepresent in a molar ratio of 1:3.

In another method, Method 83, the present disclosure provides a method,as provided by Method 73, wherein the stem cell is an embryonic stemcell, an adult stem cell, an induced pluripotent stem cell, or ahematopoietic stem cell.

In another method, Method 84, the present disclosure provides a method,as provided by Method 73, wherein the stem cell is a human stem cell.

In another method, Method 85, the present disclosure provides an invitro method for generating a universal donor cell, the methodcomprising delivering to a stem cell: (a) a first ribonucleoprotein(RNP) complex comprising an RNA-guided nuclease and a guide RNA (gRNA)targeting a target site in a beta-2 microglobulin (B2M) gene locus; (b)a first vector comprising a nucleic acid, the nucleic acid comprising:(i) a nucleotide sequence encoding a first tolerogenic factor; (ii) anucleotide sequence consisting essentially of SEQ ID NO: 7 and havingsequence homology with a genomic region located left and within 50nucleobases of the target site in the B2M gene locus; and (iii) anucleotide sequence consisting essentially of SEQ ID NO: 13 and havingsequence homology with a genomic region located right and within 50nucleobases of the target site in the B2M gene locus, wherein (i) isflanked by (ii) and (iii); wherein the B2M gene locus is cleaved at thetarget site and the nucleic acid comprising the nucleotide sequenceencoding the first tolerogenic factor is inserted into the B2M genelocus, thereby disrupting the B2M gene; (c) a second RNP complexcomprising an RNA-guided nuclease and a gRNA targeting a target site ina thioredoxin interacting protein (TXNIP) gene locus; and (d) a secondvector comprising a nucleic acid, the nucleic acid comprising: (i) anucleotide sequence encoding a second tolerogenic factor; (ii) anucleotide sequence consisting essentially of SEQ ID NO: 25 and havingsequence homology with a genomic region located left and within 50nucleobases of the target site in the TXNIP gene locus; and (iii) anucleotide sequence consisting essentially of SEQ ID NO: 32 and havingsequence homology with a genomic region located right and within 50nucleobases of the target site in the TXNIP gene locus, wherein (i) isflanked by (ii) and (iii); wherein the TXNIP gene locus is cleaved atthe target site and the nucleic acid comprising the nucleotide sequenceencoding the second tolerogenic factor is inserted into the TXNIP genelocus, thereby disrupting the TXNIP gene and generating a universaldonor cell, wherein the universal donor cell has increased immuneevasion and/or cell survival compared to a control cell.

In another method, Method 85A, the present disclosure provides a method,as provided by Method 85, wherein the nucleic acid in (b) is insertedinto the B2M gene locus within 50 base pairs of the target site and/orwherein the nucleic acid in (d) is inserted into the TXNIP gene locuswithin 50 base pairs of the target site.

In another method, Method 86, the present disclosure provides a method,as provided by Method 85, wherein the control cell is a wild type cellor a cell that does not comprise the inserted nucleic acid.

In another method, Method 87, the present disclosure provides a method,as provided by Method 85, the disrupted B2M gene has reduced oreliminated expression of B2M, and the disrupted TXNIP gene has reducedor eliminated expression of TXNIP.

In another method, Method 88, the present disclosure provides a method,as provided by Method 85, wherein the gRNA of the first RNP complexcomprises a spacer sequence corresponding to a sequence consisting ofSEQ ID NO: 1-3 or 35-44, and the gRNA of the second RNP complexcomprises a spacer sequence corresponding to a sequence consisting ofSEQ ID NO: 15-24.

In another method, Method 89, the present disclosure provides a method,as provided by Method 85, wherein the gRNA of the first RNP complexcomprises a spacer sequence corresponding to a sequence consisting ofSEQ ID NO: 2, and the gRNA of the second RNP complex comprises a spacersequence corresponding to a sequence consisting of SEQ ID NO: 20.

In another method, Method 90, the present disclosure provides a method,as provided by Method 85, wherein the first vector is a plasmid vector,and the second vector is a plasmid vector.

In another method, Method 91, the present disclosure provides a method,as provided by Method 85, wherein the first tolerogenic factor isprogrammed death-ligand 1 (PD-L1), and the second tolerogenic factor isHLA class I histocompatibility antigen, alpha chain E (HLA-E).

In another method, Method 92, the present disclosure provides a method,as provided by Method 91, wherein the nucleotide sequence encoding PD-L1consists essentially of SEQ ID NO: 11.

In another method, Method 93, the present disclosure provides a method,as provided by Method 91, wherein the nucleotide sequence encoding HLA-Ecomprises a sequence encoding a HLA-E trimer comprising a B2M signalpeptide fused to an HLA-G presentation peptide fused to a B2M membraneprotein fused to HLA-E without its signal peptide, and the sequenceencoding the HLA-E trimer consists essentially of SEQ ID NO: 55.

In another method, Method 94, the present disclosure provides a method,as provided by Method 85, wherein the nucleotide sequence encoding thefirst tolerogenic factor is operably linked to an exogenous promoter,and the nucleotide sequence encoding the second tolerogenic factor isoperably linked to an exogenous promoter.

In another method, Method 95, the present disclosure provides a method,as provided by Method 94, wherein the exogenous promoter is a CMV, EF1α,PGK, CAG, or UBC promoter.

In another method, Method 96, the present disclosure provides a method,as provided by Method 85, wherein each of the first RNP complex and thesecond RNP complex comprises a molar ratio of RNA-guided nuclease togRNA of 1:3.

In another method, Method 97, the present disclosure provides a method,as provided by Method 85, wherein the RNA-guided nuclease of each thefirst RNP complex and the second RNP complex is a Cas9 nuclease.

In another method, Method 98, the present disclosure provides a method,as provided by Method 97, wherein the Cas9 nuclease is linked to atleast one nuclear localization signal.

In another method, Method 99, the present disclosure provides a method,as provided by Method 85, wherein the stem cell is an embryonic stemcell, an adult stem cell, an induced pluripotent stem cell, or ahematopoietic stem cell.

In another method, Method 100, the present disclosure provides a method,as provided by Method 85, wherein the stem cell is a human stem cell.

In another method, Method 101, the present disclosure provides an invitro method for generating a universal donor cell, the methodcomprising delivering to a stem cell: (a) a first ribonucleoprotein(RNP) complex comprising an RNA-guided nuclease and a guide RNA (gRNA)targeting a target site in a beta-2 microglobulin (B2M) gene locus; (b)a first vector comprising a nucleic acid, the nucleic acid comprising:(i) a nucleotide sequence encoding a first tolerogenic factor; (ii) anucleotide sequence having sequence homology with a genomic regionlocated left and within 50 nucleobases of the target site in the B2Mgene locus; and (iii) a nucleotide sequence having sequence homologywith a genomic region located right and within 50 nucleobases of thetarget site in the B2M gene locus, wherein (i) is flanked by (ii) and(iii) and the first vector comprises a nucleotide sequence consisting ofSEQ ID NO: 33; wherein the B2M gene locus is cleaved at the target siteand the nucleic acid comprising the nucleotide sequence encoding thefirst tolerogenic factor is inserted into the B2M gene locus within,thereby disrupting the B2M gene; (c) a second RNP complex comprising anRNA-guided nuclease and a gRNA targeting a target site in a thioredoxininteracting protein (TXNIP) gene locus; and (d) a second vectorcomprising a nucleic acid, the nucleic acid comprising: (i) a nucleotidesequence encoding a second tolerogenic factor; (ii) a nucleotidesequence having sequence homology with a genomic region located left andwithin 50 nucleobases of the target site in the TXNIP gene locus; and(iii) a nucleotide sequence having sequence homology with a genomicregion located right and within 50 nucleobases of the target site in theTXNIP gene locus, wherein (i) is flanked by (ii) and (iii) and thesecond vector that comprises a nucleotide sequence consisting of SEQ IDNO: 34 or 56 wherein the TXNIP gene locus is cleaved at the target siteand the nucleic acid comprising the nucleotide sequence encoding thesecond tolerogenic factor is inserted into the TXNIP gene locus, therebydisrupting the TXNIP gene and generating a universal donor cell, whereinthe universal donor cell has increased immune evasion and/or cellsurvival compared to a control cell.

In another method, Method 101A, the present disclosure provides amethod, as provided by Method 101, wherein the nucleic acid in (b) isinserted into the B2M gene locus within 50 base pairs of the target siteand/or wherein the nucleic acid in (d) is inserted into the TXNIP genelocus within 50 base pairs of the target site.

In another method, Method 102, the present disclosure provides a method,as provided by Method 101, wherein the control cell is a wild type cellor a cell that does not comprise the inserted nucleic acid.

In another method, Method 103, the present disclosure provides a method,as provided by Method 10, wherein the disrupted B2M gene has reduced oreliminated expression of B2M, and the disrupted TXNIP gene has reducedor eliminated expression of TXNIP.

In another method, Method 104, the present disclosure provides a method,as provided by Method 101, wherein the gRNA of the first RNP complexcomprises a spacer sequence corresponding to a sequence consisting ofSEQ ID NO: 1-3 or 35-44, and the gRNA of the second RNP complexcomprises a spacer sequence corresponding to a sequence consisting ofSEQ ID NO: 15-24.

In another method, Method 105, the present disclosure provides a method,as provided by Method 101, wherein the gRNA of the first RNP complexcomprises a spacer sequence corresponding to a sequence consisting ofSEQ ID NO: 2, and the gRNA of the second RNP complex comprises a spacersequence corresponding to a sequence consisting of SEQ ID NO: 20.

In another method, Method 106, the present disclosure provides a method,as provided by Method 101, wherein the first vector is a plasmid vector,and the second vector is a plasmid vector.

In another method, Method 107, the present disclosure provides a method,as provided by Method 101, wherein the first tolerogenic factor isprogrammed death-ligand 1 (PD-L1), and the second tolerogenic factor isHLA class I histocompatibility antigen, alpha chain E (HLA-E).

In another method, Method 108, the present disclosure provides a method,as provided by Method 101, wherein each of the first RNP complex and thesecond RNP complex comprises a molar ratio of RNA-guided nuclease togRNA of 1:3.

In another method, Method 109, the present disclosure provides a method,as provided by Method 101, wherein the RNA-guided nuclease of each thefirst RNP complex and the second RNP complex is a Cas9 nuclease.

In another method, Method 110, the present disclosure provides a method,as provided by Method 109, wherein the Cas9 nuclease is linked to atleast one nuclear localization signal.

In another method, Method 111, the present disclosure provides a method,as provided by Method 101, wherein the stem cell is an embryonic stemcell, an adult stem cell, an induced pluripotent stem cell, or ahematopoietic stem cell.

In another method, Method 112, the present disclosure provides a method,as provided by Method 101, wherein the stem cell is a human stem cell.

In a first process, Process 1, the present disclosure provides a processfor generating universal donor cells, the process comprising: (a)modifying stem cells by inserting a nucleotide sequence encodingprogrammed death-ligand 1 (PD-L1) within or near a gene encoding beta-2microglobulin (B2M), thereby generating PD-L1 positive cells; (b)enriching for PD-L1 positive cells; (c) modifying the PD-L1 positivecells from (b) by inserting a nucleotide sequence encoding HLA class Ihistocompatibility antigen, alpha chain E (HLA-E) within or near a geneencoding thioredoxin interacting protein (TXNIP), thereby generatingPD-L1, HLA-E double positive cells; (d) enriching for PD-L1, HLA-Edouble positive cells; (e) single cell sorting to select for PD-L1,HLA-E double positive cells; (f) characterizing cells from (e) asuniversal donor cells; and (g) freezing the universal donor cells forlong term storage.

In another process, Process 2, the present disclosure provide a process,as provided in Process 1, wherein the modifying at (a) comprisesdelivering to the stem cells (1) a first ribonucleoprotein (RNP) complexcomprising an RNA-guided nuclease and a guide RNA (gRNA) targeting atarget site in the B2M gene locus and (2) a first vector comprising anucleic acid, the nucleic acid comprising (i) a nucleotide sequencehomologous with a region located left of the target site in the B2M genelocus, (ii) the nucleotide sequence encoding PD-L1, and (iii) anucleotide sequence homologous with a region located right of the targetsite in the B2M gene locus, wherein the B2M gene locus is cleaved at thetarget site and the nucleic acid comprising the nucleotide sequenceencoding PD-L1 is inserted into the B2M gene locus, thereby disruptingthe B2M gene.

In another process, Process 2A, the present disclosure provides amethod, as provided by Process 2, wherein the nucleic acid is insertedinto the B2M gene locus within 50 base pairs of the target site.

In another process, Process 3, the present disclosure provide a process,as provided in Process 2, wherein the RNA-guided nuclease of the firstRNP complex is a Cas9 nuclease and the gRNA of the first RNP complexcomprises a spacer sequence corresponding to a target sequenceconsisting of SEQ ID NO: 2.

In another process, Process 4, the present disclosure provide a process,as provided in Process 3, wherein the Cas9 nuclease is linked to atleast one nuclear localization signal.

In another process, Process 5, the present disclosure provide a process,as provided in Process 2, wherein the first RNP comprises a molar ratioof gRNA:RNA-guided nuclease of 3:1.

In another process, Process 6, the present disclosure provide a process,as provided in Process 2, wherein the nucleotide sequence of (a)(2)(i)consists essentially of SEQ ID NO: 7, and the nucleotide sequence of(a)(2)(iii) consists essentially of SEQ ID NO: 13.

In another process, Process 7, the present disclosure provide a process,as provided in Process 2, wherein the nucleotide sequence encoding PD-L1consists essentially of SEQ ID NO: 11.

In another process, Process 8, the present disclosure provide a process,as provided in Process 2, wherein the nucleotide sequence encoding PD-L1is operably linked to a CAG promoter.

In another process, Process 9, the present disclosure provide a process,as provided in Process 2, wherein the first vector is a plasmid vectorand comprises a nucleotide sequence consisting of SEQ ID NO: 33.

In another process, Process 10, the present disclosure provide aprocess, as provided in Process 2, wherein the delivering of (a)(1) and(a)(2) comprises electroporation.

In another process, Process 11, the present disclosure provide aprocess, as provided in Process 1, wherein the enriching for PD-L1positive cells at (b) comprises magnetic assisted cell sorting (MACS),single cell cloning, expanding said PD-L1 positive cells, or acombination thereof.

In another process, Process 12, the present disclosure provide aprocess, as provided in Process 1, wherein the modifying at (c)comprises delivering to the PD-L1 positive cells (1) a second RNPcomplex comprising an RNA-guided nuclease and a gRNA targeting a targetsite in the TXNIP gene locus and (2) a second vector comprising anucleic acid, the nucleic acid comprising (i) a nucleotide sequencehomologous with a region located left of the target site in the TXNIPgene locus, (ii) the nucleotide sequence encoding HLA-E, and (iii) anucleotide sequence homologous with a region located right of the targetsite in the TXNIP gene locus, wherein the TXNIP gene locus is cleaved atthe target site and the nucleic acid comprising the nucleotide sequenceencoding HLA-E is inserted into the TXNIP gene locus, thereby disruptingthe TXNIP gene.

In another process, Process 12A, the present disclosure provides amethod, as provided by Process 12, wherein the nucleic acid is insertedinto the TXNIP gene locus within 50 base pairs of the target site.

In another process, Process 13, the present disclosure provide aprocess, as provided in Process 12, wherein the RNA-guided nuclease ofthe second RNP complex is a Cas9 nuclease and the gRNA of the second RNPcomplex comprises a spacer sequence corresponding to a target sequenceconsisting of SEQ ID NO: 20.

In another process, Process 14, the present disclosure provide aprocess, as provided in Process 13, wherein the Cas9 nuclease is linkedto at least one nuclear localization signal.

In another process, Process 15, the present disclosure provide aprocess, as provided in Process 12, wherein the second RNP comprises amolar ratio of gRNA:RNA-guided nuclease of 3:1.

In another process, Process 16, the present disclosure provide aprocess, as provided in Process 12, wherein the nucleotide sequence of(c)(2)(i) consists essentially of SEQ ID NO: 25, and the nucleotidesequence of (c)(2)(iii) consists essentially of SEQ ID NO: 32.

In another process, Process 17, the present disclosure provide aprocess, as provided in Process 12, wherein the nucleotide sequenceencoding HLA-E comprises a sequence encoding a HLA-E trimer comprising aB2M signal peptide fused to an HLA-G presentation peptide fused to a B2Mmembrane protein fused to HLA-E without its signal peptide.

In another process, Process 18, the present disclosure provide aprocess, as provided in Process 17, wherein the sequence encoding theHLA-E trimer consists essentially of SEQ ID NO: 55.

In another process, Process 19, the present disclosure provide aprocess, as provided in Process 12, wherein the nucleotide sequenceencoding HLA-E is operably linked to a CAG promoter.

In another process, Process 20, the present disclosure provide aprocess, as provided in Process 12, wherein the second vector is aplasmid vector and comprises a nucleotide sequence consisting of SEQ IDNO: 34 or 56.

In another process, Process 21, the present disclosure provide aprocess, as provided in Process 12, wherein the delivering of (c)(1) and(c)(2) comprises electroporation.

In another process, Process 22, the present disclosure provide aprocess, as provided in Process claim 1, wherein the enriching forPD-L1, HLA-E double positive cells at (d) comprises magnetic assistedcell sorting, single cell cloning, expanding said PD-L1, HLA-E doublepositive cells, or a combination thereof.

In another process, Process 23, the present disclosure provide aprocess, as provided in Process 1, wherein the single-cell sorting at(e) comprises fluorescence-activated cell sorting (FACS), single cellcloning, expanding said single cell sorted cells, or a combinationthereof.

In another process, Process 24, the present disclosure provide aprocess, as provided in Process 1, wherein the characterizing at (f)comprises DNA analyses for zygosity and/or indel profile.

In another process, Process 25, the present disclosure provide aprocess, as provided in Process 1, wherein the characterizing at (f)comprises cell analyses for morphology, viability, karyotyping,endotoxin levels, mycoplasma levels, on/off target analysis, randomvector insertion, residual Cas9, residual vector, pluripotency status,differentiation capacity, or a combination thereof.

In another process, Process 26, the present disclosure provide aprocess, as provided in Process 1, wherein the process further comprisesfreezing prior to the characterizing at (f).

In another process, Process 27, the present disclosure provide aprocess, as provided in Process 1, further comprising in (a) expandingthe generated PD-L1 positive cells, in (c) expanding the generatedPD-L1, HLA-E double positive cells, in (e) expanding the selected PD-L1,HLA-E double positive cells, or a combination thereof.

In another process, Process 28, the present disclosure provide a processfor generating universal donor cells, the process comprising: (a)modifying stem cells by inserting a nucleotide sequence encoding a firsttolerogenic factor within or near a gene encoding a MHC-I or MHC-IIhuman leukocyte antigen or a component or a transcriptional regulator ofa MHC-I or MHC-II complex, thereby generating first tolerogenic factorpositive cells; (b) enriching for first tolerogenic factor positivecells; (c) modifying the first tolerogenic factor positive cells from(b) by inserting a nucleotide sequence encoding a second tolerogenicfactor within or near a gene encoding a survival factor, therebygenerating first tolerogenic factor positive/second tolerogenic factorpositive cells; (d) enriching for first tolerogenic factorpositive/second tolerogenic factor positive cells; (e) single cellsorting to select for first tolerogenic factor positive/secondtolerogenic factor positive cells; (f) characterizing the cells from (e)as universal donor cells; and (g) freezing the universal donor cells forlong term storage.

In another process, Process 29, the present disclosure provide aprocess, as provided in Process 28, wherein the enriching for firsttolerogenic factor positive cells at (b) comprises magnetic assistedcell sorting (MACS), single cell cloning, expanding said firsttolerogenic factor positive cells, or a combination thereof.

In another process, Process 30, the present disclosure provide aprocess, as provided in Process 28 or 29, wherein the enriching forfirst tolerogenic factor positive/second tolerogenic factor positivecells at (d) comprises magnetic assisted cell sorting, single cellcloning, expanding said first tolerogenic factor positive/secondtolerogenic factor positive cells, or a combination thereof.

In another process, Process 31, the present disclosure provide aprocess, as provided in any one of Processes 28 to 30, furthercomprising in (a) expanding the generated first tolerogenic factorpositive cells, in (c) expanding the generated first tolerogenic factorpositive/second tolerogenic factor positive cells, in (e) expanding theselected first tolerogenic factor positive/second tolerogenic factorpositive cells, or a combination thereof.

In another process, Process 32, the present disclosure provide aprocess, as provided in any one of Processes 28 to 31, wherein themodifying at (a) comprises delivering to the stem cells (1) a firstRNA-guided nuclease and a first guide RNA (gRNA) targeting a target sitein a MHC-I or MHC-II human leukocyte antigen or a component or atranscriptional regulator of a MHC-I or MHC-II complex gene locus and(2) a first vector comprising a first nucleic acid, the first nucleicacid comprising (i) a nucleotide sequence homologous with a regionlocated left of the target site in the MHC-I or MHC-II human leukocyteantigens or a component or a transcriptional regulator of a MHC-I orMHC-II complex gene locus, (ii) the nucleotide sequence encoding thefirst tolerogenic factor, and (iii) a nucleotide sequence homologouswith a region located right of the target site in the MHC-I or MHC-IIhuman leukocyte antigens or a component or a transcriptional regulatorof a MHC-I or MHC-II complex gene locus, wherein the MHC-I or MHC-IIhuman leukocyte antigen or a component or a transcriptional regulator ofa MHC-I or MHC-II complex gene locus is cleaved at the target site andthe first nucleic acid comprising the nucleotide sequence encoding firsttolerogenic factor is inserted into the MHC-I or MHC-II human leukocyteantigen or a component or a transcriptional regulator of a MHC-I orMHC-II complex gene locus, thereby disrupting the MHC-I or MHC-II humanleukocyte antigen or a component or a transcriptional regulator of aMHC-I or MHC-II complex gene.

In another process, Process 32A, the present disclosure provides amethod, as provided by Process 32, wherein the nucleic acid is insertedinto the MHC-I or MHC-II human leukocyte antigen or a component or atranscriptional regulator of a MHC-I or MHC-II complex gene locus within50 base pairs of the target site.

In another process, Process 33, the present disclosure provide aprocess, as provided in Proces 32, wherein the first RNA-guided nucleaseand the first gRNA form a first ribonucleoprotein (RNP) complex.

In another process, Process 34, the present disclosure provide aprocess, as provided in any one of Processes 28 to 33, wherein themodifying at (a) comprises delivering to the stem cells (1) a firstribonucleoprotein (RNP) complex comprising a first RNA-guided nucleaseand a first guide RNA (gRNA) targeting a target site in a MHC-I orMHC-II human leukocyte antigen or a component or a transcriptionalregulator of a MHC-I or MHC-II complex gene locus and (2) a first vectorcomprising a first nucleic acid, the first nucleic acid comprising (i) anucleotide sequence homologous with a region located left of the targetsite in the MHC-I or MHC-II human leukocyte antigen or a component or atranscriptional regulator of a MHC-I or MHC-II complex gene locus, (ii)the nucleotide sequence encoding the first tolerogenic factor, and (iii)a nucleotide sequence homologous with a region located right of thetarget site in the MHC-I or MHC-II human leukocyte antigen or acomponent or a transcriptional regulator of a MHC-I or MHC-II complexgene locus, wherein the MHC-I or MHC-II human leukocyte antigen or acomponent or a transcriptional regulator of a MHC-I or MHC-II complexgene locus is cleaved at the target site and the first nucleic acidcomprising the nucleotide sequence encoding first tolerogenic factor isinserted into the MHC-I or MHC-II human leukocyte antigen or a componentor a transcriptional regulator of a MHC-I or MHC-II complex gene locus,thereby disrupting the MHC-I or MHC-II human leukocyte antigen or acomponent or a transcriptional regulator of a MHC-I or MHC-II complexgene.

In another process, Process 34A, the present disclosure provides amethod, as provided by Process 34, wherein the nucleic acid is insertedinto the MHC-I or MHC-II human leukocyte antigen or a component or atranscriptional regulator of a MHC-I or MHC-II complex gene locus within50 base pairs of the target site.

In another process, Process 35, the present disclosure provide aprocess, as provided in any one of Processes 28 to 34, wherein the MHC-Ior MHC-II human leukocyte antigen or a component or a transcriptionalregulator of a MHC-I or MHC-II complex gene is HLA-A, HLA-B, HLA-C,HLA-DP, HLA-DM, HLA-DOA, HLA-DOB, HLA-DQ, HLA-DR, B2M, NLRC5, CIITA,RFX5, RFXAP, or RFXANK.

In another process, Process 36, the present disclosure provide aprocess, as provided in any one of Processes 28 to 35, wherein the MHC-Ior MHC-II human leukocyte antigen or a component or a transcriptionalregulator of a MHC-I or MHC-II complex gene is B2M.

In another process, Process 37, the present disclosure provide aprocess, as provided in Process 36, wherein the nucleotide sequence of(a)(2)(i) consists essentially of SEQ ID NO: 7, and the nucleotidesequence of (a)(2)(iii) consists essentially of SEQ ID NO: 13.

In another process, Process 38, the present disclosure provide aprocess, as provided in Processes 36 or 37, wherein the first gRNAcomprises a spacer sequence corresponding to a target sequenceconsisting of SEQ ID NO: 2.

In another process, Process 39, the present disclosure provide aprocess, as provided in any one of Processes 32 to 38, wherein the firstRNA-guided nuclease is a Cas9 nuclease.

In another process, Process 40 the present disclosure provide a process,as provided in Process 39, wherein the Cas9 nuclease is linked to atleast one nuclear localization signal.

In another process, Process 41, the present disclosure provide aprocess, as provided in any one of Processes 32 to 40, wherein the firstRNP comprises a molar ratio of first gRNA:first RNA-guided nuclease of3:1.

In another process, Process 42, the present disclosure provide aprocess, as provided in any one of Processes 28 to 41, wherein the firsttolerogenic factor is PD-L1, HLA-E, HLA-G, CTLA-4, or CD47.

In another process, Process 43, the present disclosure provide aprocess, as provided in any one of Processes 28 to 42, wherein thenucleotide sequence encoding the first tolerogenic factor is operablylinked to an exogenous promoter.

In another process, Process 44, the present disclosure provide aprocess, as provided in Process 43, wherein the exogenous promoter is aCMV, EF1α, PGK, CAG, or UBC promoter.

In another process, Process 45, the present disclosure provide aprocess, as provided in any one of Processes 28 to 44, wherein the firsttolerogenic factor is PD-L1.

In another process, Process 46, the present disclosure provide aprocess, as provided in Process 45, wherein the nucleotide sequenceencoding PD-L1 consists essentially of SEQ ID NO: 11.

In another process, Process 47, the present disclosure provide aprocess, as provided in Process 46, wherein the nucleotide sequenceencoding PD-L1 is operably linked to a CAG promoter.

In another process, Process 48, the present disclosure provide aprocess, as provided in any one of Processes 45 to 47, wherein the firstvector comprises a nucleotide sequence consisting of SEQ ID NO: 33.

In another process, Process 49, the present disclosure provide aprocess, as provided in any one of Processes 28 to 48, wherein themodifying at (c) comprises delivering to the stem cells (1) a secondRNA-guided nuclease and a second guide RNA (gRNA) targeting a targetsite in a survival factor gene locus and (2) a second vector comprisinga second nucleic acid, the second nucleic acid comprising (i) anucleotide sequence homologous with a region located left of the targetsite in the survival factor gene locus, (ii) the nucleotide sequenceencoding the second tolerogenic factor, and (iii) a nucleotide sequencehomologous with a region located right of the target site in thesurvival factor gene locus, wherein the survival factor gene locus iscleaved at the target site and the second nucleic acid comprising thenucleotide sequence encoding the second tolerogenic factor is insertedinto the survival factor gene locus, thereby disrupting the survivalfactor gene.

In another process, Process 49A, the present disclosure provides amethod, as provided by Process 49, wherein the nucleic acid is insertedinto the survival factor gene locus within 50 base pairs of the targetsite.

In another process, Process 50, the present disclosure provide aprocess, as provided in Process 49, wherein the second RNA-guidednuclease and the second gRNA form a second ribonucleoprotein (RNP)complex.

In another process, Process 51, the present disclosure provide aprocess, as provided in any one of Processes 28 to 48, wherein themodifying at (c) comprises delivering to the first tolerogenic factorpositive cells (1) a second ribonucleoprotein (RNP) complex comprising asecond RNA-guided nuclease and a second guide RNA (gRNA) targeting atarget site in a survival factor gene locus and (2) a second vectorcomprising a second nucleic acid, the second nucleic acid comprising (i)a nucleotide sequence homologous with a region located left of thetarget site in the survival factor gene locus, (ii) the nucleotidesequence encoding the second tolerogenic factor, and (iii) a nucleotidesequence homologous with a region located right of the target site inthe second survival factor gene locus, wherein the survival factor genelocus is cleaved at the target site and the second nucleic acidcomprising the nucleotide sequence encoding the second tolerogenicfactor is inserted into the survival factor gene locus, therebydisrupting the survival factor gene.

In another process, Process 51A, the present disclosure provides amethod, as provided by Process 51, wherein the nucleic acid is insertedinto the survival factor gene locus within 50 base pairs of the targetsite.

In another process, Process 52, the present disclosure provide aprocess, as provided in any one of Processes 28 to 51, wherein thesurvival gene is TXNIP, ZNF143, FOXO1, JNK, or MANF.

In another process, Process 53, the present disclosure provide aprocess, as provided in Process 52, wherein the survival gene is TXNIP.

In another process, Process 54, the present disclosure provide aprocess, as provided in Process 53, wherein the second gRNA comprises aspacer sequence corresponding to a target sequence consisting of SEQ IDNO: 20.

In another process, Process 55, the present disclosure provide aprocess, as provided in Process 52 or 53, wherein the nucleotidesequence of (c)(2)(i) consists essentially of SEQ ID NO: 25, and thenucleotide sequence of (c)(2)(iii) consists essentially of SEQ ID NO:32.

In another process, Process 56, the present disclosure provide aprocess, as provided in any one of Processes 49 to 55, wherein thesecond RNA-guided nuclease is a Cas9 nuclease.

In another process, Process 57, the present disclosure provide aprocess, as provided in Process 56, wherein the Cas9 nuclease is linkedto at least one nuclear localization signal.

In another process, Process 58, the present disclosure provide aprocess, as provided in any one of Processes 49 to 57, wherein thesecond RNP comprises a molar ratio of second gRNA:second RNA-guidednuclease of 3:1.

In another process, Process 59, the present disclosure provide aprocess, as provided in any one of Processes 49 to 58, wherein thesecond tolerogenic factor is PD-L1, HLA-E, HLA-G, CTLA-4, or CD47.

In another process, Process 60, the present disclosure provide aprocess, as provided in any one of Processes 28 to 59, wherein thenucleotide sequence encoding the second tolerogenic factor is operablylinked to an exogenous promoter.

In another process, Process 61, the present disclosure provide aprocess, as provided in Process 60, wherein the exogenous promoter is aCMV, EF1α, PGK, CAG, or UBC promoter.

In another process, Process 62, the present disclosure provide aprocess, as provided in any one of Processes 28 to 61, wherein thesecond tolerogenic factor is HLA-E.

In another process, Process 63, the present disclosure provide aprocess, as provided in Process 62, wherein the nucleotide sequenceencoding HLA-E comprises a sequence encoding a HLA-E trimer comprising aB2M signal peptide fused to an HLA-G presentation peptide fused to a B2Mmembrane protein fused to HLA-E without its signal peptide.

In another process, Process 64, the present disclosure provide aprocess, as provided in Process 63, wherein the sequence encoding theHLA-E trimer consists essentially of SEQ ID NO: 55.

In another process, Process 65, the present disclosure provide aprocess, as provided in Process 63 or 64, wherein the nucleotidesequence encoding HLA-E is operably linked to a CAG promoter.

In another process, Process 66, the present disclosure provide aprocess, as provided in any one of Processes 62 to 65, wherein thesecond vector comprises a nucleotide sequence consisting of SEQ ID NO:34 or 56.

In another process, Process 67, the present disclosure provide aprocess, as provided in any one of Processes 28 to 66, wherein thesingle-cell sorting at (e) comprises fluorescence-activated cell sorting(FACS), single cell cloning, expanding said single cell sorted cells, ora combination thereof.

In another process, Process 68, the present disclosure provide aprocess, as provided in any one of Processes 28 to 67, wherein thecharacterizing at (f) comprises DNA analyses for zygosity and/or indelprofile.

In another process, Process 69, the present disclosure provide aprocess, as provided in any one of Processes 28 to 68, wherein thecharacterizing at (f) comprises cell analyses for morphology, viability,karyotyping, endotoxin levels, mycoplasma levels, on/off targetanalysis, random vector insertion, residual Cas9, residual vector,pluripotency status, differentiation capacity, or a combination thereof.

In another process, Process 70, the present disclosure provide aprocess, as provided in any one of Processes 28 to 69, wherein theprocess further comprises freezing prior to the characterizing at (f).

VII. Examples

The examples below describe generation and characterization of specificuniversal donor cells according to the present disclosure.

Example 1: Cell Maintenance and Expansion

Maintenance of hESC/hiPSCs. Cells of human embryonic stem cell lineCyT49 (proprietary hES cell line, ViaCyte, Inc., San Diego, Calif.) weremaintained, cultured, passaged, proliferated, and plated as described inSchulz et al. (2012) PLoS ONE 7(5): e37004. CyT49 cells weredisassociated using ACCUTASE® (Stemcell Technologies 07920 orequivalent).

Human induced pluripotent stem cells (hiPSCs), such as the TC1133 cellline (Lonza), were maintained in StemFlex Complete (Life Technologies,A3349401) on BIOLAMININ 521 CTG (BioLamina Cat #CT521) coated tissueculture plates. The plates were pre-coated with a 1:10 or a 1:20dilution of BIOLAMININ in DPBS, calcium, magnesium (Life Technologies,14040133) for 2 hours at 37° C. The cells were fed daily with StemFlexmedia. For passaging of the cells, same densities of cells as for CyT49were used. For plating of the cells as single cells, the cells wereplated with 1% RevitaCell™ Supplement (100×) (Thermofisher Cat#A2644501) in StemFlex on BIOLAMININ coated plates.

Single cell cloning of hPSCs. For single cell cloning, hPSCs (hESCs orhiPSCs) were fed with StemFlex Complete with Revitacell (for finalconcentration of 1× Revitacell) 3-4 hours prior to dissociation withACCUTASE®. Following dissociation, the cells were sorted as a singlecell per well of a BIOLAMININ coated 96 well tissue culture plate. TheWOLF FACS-sorter (Nanocellect) was used to sort single cells into thewells. The plates were pre-filled with 100-200 μL of StemFlex Completewith Revitacell. Three days post cell seeding, the cells were fed withfresh StemFlex and continued to be fed every other day with 100-200 μLof media. After 10 days of growth, the cells were fed daily withStemFlex until day 12-14. At this time, the plates were dissociated withACCUTASE® and the collected cell suspensions were split 1:2 with halfgoing into a new 96 well plate for maintenance and half going into a DNAextraction solution QuickExtract™ DNA Extraction Solution (Lucigen).Following DNA extraction, PCR was performed to assess presence orabsence of desired gene edits at the targeted DNA locus. Sangersequencing was used to verify desired edits.

Expansion of single cell derived hPSCs clones. For CyT49 (ViaCyte),successfully targeted clones were passaged onto 24-well plates with pure10% XF KSR A10H10 media but on BIOLAMININ-coated plates. Following the24-well stage, CyT49 clones were passaged as described in Schulz et al.(2012) PLoS ONE 7(5): e37004.

For hiPSCs (TC1133), cells were maintained in StemFlex Completethroughout the cloning and regular maintenance processes onBIOLAMININ-coated plates with Revitacell at the passaging stages.

Example 2: Generation of B2M Knock-Out (KO) Human Pluripotent Stem Cells(hPSCs)

Guide RNA (gRNA) selection for B2M in hPSCs. Three B2M targeting gRNAswere designed for targeting exon 1 of the B2M coding sequence. ThesegRNAs had predicted low off-target scores based on sequence homologyprediction using gRNA design software. The target sequences of the gRNAsare presented in Table 1. A gRNA comprises RNA sequence corresponding tothe target DNA sequence.

TABLE 1 B2M gRNA Target Sequences Target Sequence SEQ ID Name (5′-3′)NO: PAM B2M-1 gRNA GCTACTCTCTCTTTCTGGCC 1 TGG (Exon 1_T12) B2M-2 gRNAGGCCGAGATGTCTCGCTCCG 2 TGG (Exon 1_T2) B2M-3 gRNA CGCGAGCACAGCTAAGGCCA 3CGG (Exon 1_T8) Exon 1_T1 TATAAGTGGAGGCGTCGCGC 35 TGG Exon 1_T3GAGTAGCGCGAGCACAGCTA 36 AGG Exon 1_T4 ACTGGACGCGTCGCGCTGGC 37 GGGExon 1_T5 AAGTGGAGGCGTCGCGCTGG 38 CGG Exon 1_T6 GGCCACGGAGCGAGACATCT 39CGG Exon 1_T7 GCCCGAATGCTGTCAGCTTC 40 AGG Exon 1_T9 CTCGCGCTACTCTCTCTTTC41 TGG Exon 1_T10 TCCTGAAGCTGACAGCATTC 42 GGG Exon 1_T11TTCCTGAAGCTGACAGCATT 43 CGG Exon 1_T13 ACTCTCTCTTTCTGGCCTGG 44 AGG

To assess their cutting efficiency in hPSCs, CyT49 cells (ViaCyteproprietary hES cell line) were electroporated using the NeonElectroporator (Neon Transfection System ThermoFisher Cat #MPK5000) witha ribonucleoprotein (RNP) mixture of Cas9 protein (Biomay) and guide RNA(Synthego) (See Table 3 for gRNA sequences) at a molar ratio of 3:1(gRNA:Cas9) with absolute values of 125 pmol Cas9 and 375 pmol gRNA. Toform the RNP complex, gRNA and Cas9 were combined in one vessel withR-buffer (Neon Transfection System 100 μL Kit ThermoFisher Cat#MPK10096) to a total volume of 25 μL and incubated for 15 min at RT.Cells were dissociated using ACCUTASE®, then resuspended in DMEM/F12media (Gibco, cat #11320033), counted using an NC-200 (Chemometec) andcentrifuged. A total of 1×10⁶ cells were resuspended with the RNPcomplex and R-buffer was added to a total volume of 125 μL. This mixturewas then electroporated with 2 pulses for 30 ms at 1100 V. Followingelectroporation, the cells were pipetted out into an Eppendorf tubefilled with StemFlex media with RevitaCell. This cell suspension wasthen plated into tissue culture dishes pre-coated with BIOLAMININ 521CTG at 1:20 dilution. Cells were cultured in a normoxia incubator (37°C., 8% CO₂) for 48 hours. After 48 hours, genomic DNA was harvested fromthe cells using QuickExtract (Lucigen, Middleton, Wis.; Cat #QE09050).

PCR for the target B2M sequence was performed and the resultingamplified DNA was assessed for cutting efficiency by TIDE analysis. PCRfor relevant regions was performed using Platinum Taq Supermix(Invitrogen, cat #125320176 and Cat #11495017). The sequences of the PCRprimers are presented in Table 2; and the cycling conditions provided inTable 3.

TABLE 2 B2M TIDE Primers SEQ ID Name Type Sequence (5′-3′) NO: B2MF2forward CAGACAGCAAACTCACCCAG 4 B2MR2 reverse AAACTTTGTCCCGACCCTCC 5

TABLE 3 B2M PCR Cycling Parameters Step Temperature Time CyclesDenaturation 94° C. 2 min  1 Denaturation 94° C. 15 sec 38 Annealing 55°C.° C. 30 sec Extension 68° C. 45 sec Elongation 68° C. 5 min  1 Hold 4hold

The resulting amplicons were submitted for PCR cleanup and Sangersequencing. Sanger sequencing results were input into Tsunami softwarealong with the guide sequence. Indel percentages and identities werecalculated by the software. Particular gRNAs were then selected based ontheir indel frequency in hPSCs. FIG. 1 shows the cutting efficiency ofB2M-1, B2M-2, and B2M-3 gRNAs.

Off-targets of the selected gRNAs were assessed in the stem cell-derivedDNA using hybrid capture analysis of the sequence similarity predictedsites. B2M-2 and B2M-3 guides did not show detectable off-targeteffects. B2M-2 gRNA was chosen for further clone generation due to itshigh on-target activity and undetectable off-target activity.

B2M KO hPSC clone generation and characterization. Using B2M-2 gRNA,CyT49 hESCs (ViaCyte) were electroporated and single-cell sorted 3 dayspost electroporation using the WOLF FACS-sorter (Nanocellect) intoBIOLAMININ 521 CTG coated 96-well plates with StemFlex and Revitacell.Plated single cells were grown in a normoxia incubator (37° C., 8% CO₂)with every other day media changes until colonies were large enough tobe re-seeded as single cells. When confluent, samples were split formaintenance and genomic DNA extraction.

The B2M KO state of clones was confirmed via PCR and Sanger sequencing.The resulting DNA sequences of the target B2M region were aligned inSnapgene software to determine indel identity and zygosity. Clones withdesired edits were expanded and further verified through flow cytometryassessment for B2M expression (See Table 4 for list of antibodiesutilized). Clones were assessed with or without Interferon-gammatreatment (25 ng/mL, R & D Systems, 285-IF). FIG. 2A shows B2Mexpression in wild type cells and FIG. 2B presents B2M expression in B2MKO cells. Karyotypic status of clones was evaluated through Cell LineGenetics service (Madison, Wis.) and normal karyotype was reported.

TABLE 4 Antibodies for Pluripotency Flow Cytometry Antigen CloneFluorophore Manufacturer Catalog # Oct3/4 40/3 Alexa 647 BD Bioscience560329 SOX2 030-678 PE BD Bioscience 562195 B2M 2M2 PE Biolegend 316305HLA-ABC W6/32 Alexa 488 Biolegend 311415 mIgG1 N/A PE BD Bioscience555749 kappa PD-L1 B7-H1 Alexa-488 ThermoFisher 53-5983-42 HLA-E 3D12 PEThermoFisher 12-9953-42

Clones were confirmed to retain pluripotency through intracellular flowcytometry for pluripotency markers OCT4 and SOX2. Confirmed pluripotentclones were differentiated to pancreatic endocrine progenitors usingpreviously established methods (Schulz et al. (2012) PLoS ONE 7(5):e37004).

Example 3: Generation of B2M KO/PD-L1 Knock-in (KI) Human PluripotentStem Cells (hPSCs)

Design of B2M KO/PD-L1 KI strategy. Plasmid design to insert PD-L1(CD274) into the B2M locus was made such that the starting codon of B2Mwas removed after undergoing homology directed repair (HDR) to insertPD-L1, nullifying any chance of partial B2M expression. FIG. 3 presentsa schematic of the plasmid and Table 5 identifies the elements andlocations therein. The donor plasmid contained a CAGGS promoter drivencDNA of PD-L1 flanked by 800 base pair homology arms with identicalsequence to the B2M locus around exon 1. The complete sequence of theplasmid comprises SEQ ID NO: 33.

TABLE 5 Elements of B2M-CAGGS-PD-L1 Donor Plasmid Element Location (sizein bp) SEQ ID NO: Left ITR 1-130 (130)  6 LHA-B2M 145-944 (800)  7 CMVenhancer 973-1352 (380)  8 chicken β-actin promoter 1355-1630 (276)  9chimeric intron 1631-2639 (1009) 10 PD-L1 2684-3556 (873) 11 bGH poly(A)signal 3574-3798 (225) 12 RHA-B2M 3805-4604 (800) 13 Right ITR 4646-4786(141) 14 Entire plasmid 7133 bp 33

The B2M-2 gRNA was used to facilitate insertion of the PD-L1 transgeneat the targeted B2M locus. The PD-L1 donor plasmid was introduced alongwith the RNP complex made up of the B2M targeting gRNA and Cas9 protein.Per 1 million of CyT49 cells (ViaCyte), 4 μg of plasmid DNA wasdelivered along with the RNP. Electroporation was carried out asdescribed in Example 2. Seven days post electroporation, the cells weresorted for PD-L1 surface expression using the WOLF FACS-sorter(Nanocellect) into BIOLAMININ 521 CTG coated 96-well plates withStemFlex with Revitacell. For FACS-sorting, unedited cells served as anegative control. PD-L1 positive cells were selected for sorting andsingle cell cloning.

To detect the PD-L1 surface expression, anti-PD-L1 fluorescentantibodies were used (see Table 4). Plated single cells were grown in anormoxia incubator (37° C., 8% CO₂) with every other day media changesuntil colonies were large enough to be re-seeded as single cells. Whenconfluent, samples were split for maintenance and genomic DNAextraction.

Correctly targeted clones were identified via PCR for the PD-L1 knock-in(KI) insertion using primers that amplify a region from outside theplasmid homology arms to the PD-L1 cDNA insertion enabling amplificationof the KI integrated DNA only. On-target insertion was tested forzygosity by PCR to assess if KI occurred in a heterozygous or homozygousmanner. If a heterozygous clone was identified, the KI negative allelewas sent for Sanger sequencing to verify that it contained aB2M-disrupting indel in the non-KI allele. The correct KI clones withfull B2M disruption (either via KI insertion or indel formation) wereexpanded in increasing tissue culture formats until a population size of30 million cells was reached. Approximately 10 clones were expanded inthis manner and confirmed to be pluripotent by testing for OCT4 and SOX2via intracellular flow cytometry (FIG. 4). Clones that passed the abovetests, were then tested further for karyotypic analysis (Cell LineGenetics), as described below. Additionally, the clones were then testedfor their competence to differentiate to pancreatic endoderm precursors(PEC) via the established protocol (Schulz et al. (2012) PLoS ONE 7(5):e37004), as described below. The loss of B2M was further confirmed bylack of expression of B2M with or without interferon-gamma treatment (25ng/mL, R & D Systems, 285-IF) through flow cytometry. FIGS. 5A and 5Bshow PD-L1 expression in wildtype and B2M KO/PD-L1 KI cells,respectively.

Example 4: Karyotype Analysis of Edited Clones

C-Band Karyotyping Analysis of Edited Embryonic Stem (ES) Cells. 1million of edited ES cells were passaged into a T-25 culture flask withculture media (DMEM/F12+10% Xeno-free KSR with 10 ng/mL Activin and 10ng/mL Heregulin). After culturing overnight, three T25 culture flaskswere shipped to Cytogenetics Laboratory (Cell Line Genetics, Inc.) forKaryotyping analysis; FISH analysis for Chromosome 1, 12, 17, 20; andarray comparative genomic hybridization (aCGH) analysis with standard8×60K array. The G-banding results of selected cells electroporated withnon-cutting guides (“NCG”), B2M KO clones, and B2M KO/PD-L1 KI clones(“V1-A”) are shown in Table 6.

TABLE 6 G-band Karyotyping Results aCGH Karyotyping FISH array Cell LineType Passage analysis analysis analysis NCG#1 non-cutting P36 NormalNormal PASS guide NCG#2 non-cutting P36 Normal Normal PASS guide B2M B2MKO P38 Normal Normal PASS KO#1 B2M B2M KO P36 Normal Normal PASS KO#2B2M B2M KO P36 Normal Normal PASS KO#3 V1-A003 B2M KO/ P37 Normal NormalPASS PD-L1 KI V1-A004 B2M KO/ P38 Normal Normal PASS PD-L1 KI V1-A007B2M KO/ P37 Normal Normal PASS PD-L1 KI V1-A008 B2M KO/ P38 NormalNormal PASS PD-L1 KI

Example 5: Differentiation of Edited Human Embryonic Stem Cells toPancreatic Endoderm Cells (PECs)

Maintenance of edited human embryonic stem cells (ES). The edited humanembryonic stem cells at various passages (P38-42) were seeded at 33,000cells/cm² for a 4-day passage or 50,000 cells/cm² for a 3-day passagewith hESM medium (DMEM/F12+10% KSR+10 ng/mL Activin A and 10 ng/mLHeregulin) and final 10% human AB serum.

Aggregation of edited human embryonic stem cells for PECsdifferentiation. The edited ES were dissociated into single cells withACCUTASE® and then centrifuged and resuspended in 2% StemPro (Cat#A1000701, Invitrogen, CA) in DMEM/F12 medium at 1 million cells per ml,and total 350-400 million of cells were seeded in one 850 cm² rollerbottle (Cat #431198, Corning, N.Y.) with rotation speed at 8 RPM±0.5 RPMfor 18-20 hours before differentiation. The ES aggregates from editedhuman embryonic stem cells were differentiated into pancreatic lineagesusing in roller bottles as described in Schulz et al. (2012) PLoS ONE7(5): e37004.

Example 6: Characterization of Differentiated Pancreatic Endoderm Cells(PECs)

Flow cytometry for FOXA2 and SOX17 at Stage 1 (DE) and CHGA, PDX1 andNKX6.1 at PEC stage. hESC-derived stage 1 aggregates, or hESC-derivedpancreatic aggregates, were washed with PBS and then enzymaticallydissociated to single cells suspension at 37° C. using ACCUMAX™ (Catalog#A7089, Sigma, MO). MACS Separation Buffer (Cat #130-091-221, MiltenyiBiotec, North Rhine-Westphalia, Germany) was added and the suspensionwas passed through a 40 μm filter and pelleted. For intracellular markerstaining, cells were fixed for 30 mins in 4% (wt/v) paraformaldehyde,washed in FACS Buffer (PBS, 0.1% (wt/v) BSA, 0.1% (wt/v) NaN₃) and thencells were permeabilized with Perm Buffer (PBS, 0.2% (v/v) Triton X-100(Cat #A16046, Alfa Aesar, MA), 5% (v/v) normal donkey serum, 0.1% (wt/v)NaN₃) for 30 mins on ice and then washed with washing buffer (PBS, 1%(wt/v) BSA, 0.1% (wt/v) NaN₃). Cells were incubated with primaryantibodies (Table 7) diluted with Block Buffer (PBS, 0.1% (v/v) TritonX-100, 5% (v/v) normal donkey serum, 0.1% (wt/v) NaN₃) overnight at 4°C. Cells were washed in IC buffer and then incubated with appropriatesecondary antibodies for 60 mins at 4° C. Cells were washed in IC bufferand then in FACS Buffer. Flow cytometry data were acquired with NovoCyteFlow Cytometer (ACEA Biosciences, Brussels). Data were analyzed usingFlowJo software (Tree Star, Inc.). Intact cells were identified based onforward (low angle) and side (orthogonal, 90°) light scatter. Backgroundwas estimated using antibody controls and undifferentiated cells. In thefigures, a representative flow cytometry plot is shown for one of thesub-populations. Numbers reported in the figures represent thepercentage of total cells from the intact cells gate.

TABLE 7 Antibodies for flow cytometry for characterization ofdifferentiated PECs Antigen Fluorophore Source Dilution SOX17 AF647 BDBioscience 1:50   (Cat#562594) FOXA2 PE Miltenyi Biotechnology 1:10  (Cat#130-107-773) PDX1 PE BD Bioscience 1:2.5  (Cat#562161) NKX6.1 AF647BD Bioscience 1:2.5  (Cat#563338) CHGA AF405 Novus 1:1000 (Cat#NBP2-33198AF405)

At DE stage, the population of FOXA2 and SOX17 double positive cellswere more than 90% of total cells from CyT49 wild types differentiatedcells. The PD-L1 KI/B2M KO and B2M KO cells showed comparable percentageof DE compared to wild type cells (FIG. 6 and FIG. 7).

At PECs stage, flow cytometry for chromogranin (CHGA), PDX1 and NKX6.1was performed. The heterogeneous population at PEC stage includepancreatic progenitors and early endocrine cells (FIG. 8). From the piechart of the heterogeneous population (FIG. 9), the distribution of cellpopulations from differentiated edited cells (PD-L1 KI/B2M KO or B2M KO)were very similar to wild type cells.

Targeted RNAseq. Targeted RNAseq for gene expression analysis wasperformed using Illumina TruSeq and a custom panel of oligos targeting111 genes. The panel primarily contained genes that are markers of thedevelopmental stages during pancreatic differentiation. At end of eachdifferentiation stage, 10 μL APV (aggregated pellet volume) wascollected and extracted using the Qiagen RNeasy or RNeasy 96 spin columnprotocol, including on-column DNase treatment. Quantification andquality control were performed using either the TapeStation combinedwith Qubit, or by using the Qiagen QIAxcel. 50-200 ng of RNA wasprocessed according to the Illumina TruSeq library preparation protocol,which consists of cDNA synthesis, hybridization of the custom oligopool, washing, extension, ligation of the bound oligos, PCRamplification of the libraries, and clean-up of the libraries, prior toquantification and quality control of the resulting dsDNA librariesusing either the TapeStation combined with Qubit, or by using the QiagenQIAxcel. The libraries were subsequently diluted to a concentration of 4nM and pooled, followed by denaturing, spike in of PhiX control, andfurther dilution to 10-12 pM prior to loading on the Illumina MiSeqsequencer. Following the sequencing run, initial data analysis wasperformed automatically through BaseSpace, generating raw read countsfor each of the custom probes. For each gene, these read counts werethen summed for all probes corresponding to that gene, with the additionof 1 read count (to prevent downstream divisions by 0). Normalizationwas performed to the gene SF3B2, and the reads were typically visualizedas fold change vs. Stage 0. When the data was processed for principalcomponent analysis, normalization was performed using the DEseq method.

Selected gene expression was shown in FIG. 10. The kinetic expressionpattern of FOXA2, CHGA, PDX1 and NKX6.1 from PD-L1 KI/B2M KO, or B2M KOcells was similar to wild type cells.

Confirmation of B2M and PD-L1 expression at PEC stage. At PEC stage,differentiated aggregates were treated with or without interferon-gamma(50 ng/ml) for 48 hours. The aggregates washed with PBS and thenenzymatically dissociated into single cells suspension at 37° C. usingACCUMAX™ (Catalog #A7089, Sigma, MO). MACS Separation Buffer (Cat#130-091-221, Miltenyi Biotec, North Rhine-Westphalia, Germany) wasadded and the suspension was passed through a 40 μm filter and pelleted.For surface marker staining, dissociated cells were incubated withfluorescent-conjugated antibody diluted in MACS Separation Buffer for 20mins and then washed in MACS Separation Buffer. Cells were resuspendedin FACS buffer for flow acquisition. Flow cytometry data were acquiredwith NovoCyte Flow Cytometer. As shown the FIGS. 11A-11F, B2M expressionwas below the detection limit in differentiated PECs from B2M KO (FIG.11B) or PD-L1 KI/B2M KO (FIG. 11C), and PD-L1 was expressed in thedifferentiated PECs from PD-L1 KI/B2M KO (FIG. 11F). In general, morethan about 90% of the PECs expressed PD-L1 indicating a homogenouspopulation of cells. Frequently, there is a loss of transgene expressionover time following differentiation of gene-edited stem cells (Hong etal., Mol. Ther., 2017, 25(1):44-53).

Immune phenotype of PEC cells. At PEC stage, differentiated aggregateswere treated with or without interferon-gamma (50 ng/ml) for 48 hours.The aggregates were harvested for MHC class I and II staining. No MHCclass II expression at PEC stage from wild type or edited cells (PD-L1KI/B2M KO and B2M KO) (FIGS. 12D-12F). The expression of HLA-ABC (MHCclass I) was low (1.3% from wild type cells) and it was highly regulatedupon IFN-γ stimulation. However, HLA-ABC was not expressed even underIFN-γ stimulation in the edited cells (PD-L1 KI/B2M KO and B2M KO) (FIG.12A-12C).

Example 7: Generation of TXNIP KO Human Pluripotent Stem Cells (hPSCs)

Guide RNA (gRNA) selection for TXNIP. Ten TXNIP targeting gRNAs weredesigned for targeting exon 1 and exon 2 of the TXNIP coding sequence(Table 8). The PAM sequences are presented in bold font in the targetsequences presented in Table 8, and the DNA sequences corresponding tothe guide sequences are presented in Table 8. These gRNAs had predictedlow off-target scores based on sequence homology prediction using gRNAdesign software.

TABLE 8 Selected TXNIP Target Sequences and gRNA Sequences TargetSequence DNA Version (5′-3′) (PAM SEQ of Guide SEQ sequence ID SequenceID Name in bold) NO: (5′-3′) NO: TXNIP_Exon GAAGCGTGTCTT 45 GAAGCGTGTCT15 1_T1 CATAGCGCAGG TCATAGCGC TXNIP_Exon TTACTCGTGTCA 46 TTACTCGTGTC 161_T21 AAGCCGTTAGG AAAGCCGTT TXNIP_Exon TGTCAAAGCCGT 47 TGTCAAAGCCG 171_T22 TAGGATCCTGG TTAGGATCC TXNIP_Exon GCCGTTAGGATC 48 GCCGTTAGGAT 181_T23 CTGGCTTGCGG CCTGGCTTG TXNIP_Exon GCGGAGTGGCTA 49 GCGGAGTGGCT 191_T25 AAGTGCTTTGG AAAGTGCTT TXNIP_Exon TCCGCAAGCCAG 50 TCCGCAAGCCA 201_T5 GATCCTAACGG GGATCCTAA TXNIP_Exon GTTCGGCTTTGA 51 GTTCGGCTTTG 212_T4 GCTTCCTCAGG AGCTTCCTC TXNIP_Exon GAGATGGTGATC 52 GAGATGGTGAT 222_T2 ATGAGACCTGG CATGAGACC TXNIP_Exon TTGTACTCATAT 53 TTGTACTCATA 232_T1 TTGTTTCCAGG TTTGTTTCC TXNIP_Exon AACAAATATGAG 54 AACAAATATGA 242_T3 TACAAGTTCGG GTACAAGTT

TXNIP KO hiPSC clone generation and characterization. To assess thecutting efficiency of these gRNAs in hiPSCs, TC1133 hiPSC cells wereelectroporated using the Neon Electroporator (Neon Transfection SystemThermoFisher Cat #MPK5000) with an RNP mixture of Cas9 protein (Biomay)and guide RNA (Synthego) at a molar ratio of 3:1 (gRNA:Cas9) withabsolute values of 125 pmol of Cas9 and 375 pmol of gRNA. To form theRNP complex, gRNA and Cas9 were combined in one vessel with R-buffer toa total volume of 25 μL and incubated for 15 min at RT. Cells weredissociated using ACCUTASE®, then resuspended in DMEM/F12 media (Gibco,cat #11320033), counted using an NC-200 (Chemometec) and centrifuged. Atotal of 1×10⁶ cells were resuspended with the RNP complex and R-bufferwas added to a total volume of 125 μL. This mixture was thenelectroporated using the parameters: 2 pulses, 30 ms, 1100 V. Followingelectroporation, the cells were pipetted out into an Eppendorf tubefilled with StemFlex media with RevitaCell. This cell suspension wasthen plated into tissue culture dishes pre-coated with BIOLAMININ 521CTG. Cells were cultured in a normoxia incubator (37° C., 8% CO₂) for 48hours. After 48 hours, genomic DNA was harvested from the cells usingQuickExtract.

PCR for the target TXNIP sequence was performed and the resultingamplified DNA was Sanger sequenced. TIDE analysis was used to analyzethe output sequencing data for indel percentages using Tsunami software.FIG. 13 shows the cutting efficiency for the TXNIP gRNAs. gRNAs werethen selected based on their indel frequency in hPSCs.

Off-targets of the most cutting efficient gRNAs were assessed in thestem cell-derived DNA using hybrid capture analysis of the sequencesimilarity predicted sites. Further experiments with TXNIP gRNA T5 wereperformed as it did not show detectable off-target effects anddemonstrated high on-target activity.

TXNIP KO hPSC clone generation and characterization. Using TXNIP gRNAT5, CyT49 hESCs (Viacyte) were electroporated and single-cell sorted at3 days post electroporation using the WOLF FACS-sorter (Nanocellect)into BIOLAMININ 521 CTG 96-well plates with StemFlex and Revitacell.Plated single cells were grown in a normoxia incubator (37° C., 8% CO₂)with every other day media changes until colonies were large enough tobe re-seeded as single cells. When confluent, samples were split formaintenance and genomic DNA extraction.

The TXNIP KO state of clones was confirmed via PCR and Sangersequencing. The resulting DNA sequences of the target TXNIP region werealigned in Snapgene software to determine indel identity and zygosity.Clones with desired edits were expanded and further verified throughflow cytometry assessment for TXNIP expression. Karyotypic status ofclones was evaluated through Cell Line Genetics service and normalkaryotype was reported (Table 9).

TABLE 9 Karyotype Analysis aCGH Karyotyping FISH array Cell Line Passageanalysis analysis analysis TXNIPKO#2  P31 Normal Normal PASS TXNIPKO#13P31 Normal Normal PASS

Clones were confirmed to retain pluripotency through intracellular flowcytometry for pluripotency markers OCT4 and SOX2. Confirmed pluripotentclones were differentiated to pancreatic endocrine progenitors usingpreviously established methods (Schulz et al. (2012) PLoS ONE 7(5):e37004).

Targeted RNAseq for gene expression analysis was performed usingIllumina TruSeq and a custom panel of oligos, as described above.Selected gene expression was shown in FIG. 20. The kinetic expressionpattern of FOXA2, CHGA, PDX1 and NKX6.1 from TXNIP KO cells was similarto wild type cells. At PECs stage, flow cytometry for chromogranin(CHGA), PDX1 and NKX6.1 was also performed. The heterogeneous populationat PEC stage included 30.6% pancreatic progenitor cells (i.e.,CHGA⁺/NKX6.1⁺/PDX1⁺) (FIG. 21).

Example 8: Generation of B2M KO/PD-L1 KI and TXNIP KO/HLA-E KI HumanPluripotent Stem Cells (hPSCs)

Design of B2M KO/PD-L1 KI and TXNIP KO/HLA-E KI strategy. Cells weregenerated in which PD-L1 coding sequence was inserted in the B2M locus(thereby knocking out the B2M gene) and HLA-E coding sequence wasinserted in the TXNIP locus (thereby knocking out the TXNIP gene).

Plasmid design to insert PD-L1 (CD274) into the B2M locus was depictedin Example 3. The donor plasmid contains a CAGGS promoter driven cDNA ofPD-L1 flanked by 800 base pair homology arms with identical sequence tothe B2M locus around exon 1. The B2M-2 gRNA was used to facilitateinsertion of the PD-L1 transgene at the targeted B2M locus. The PD-L1donor plasmid was introduced along with the RNP complex made up of theB2M targeting gRNA and Cas9 protein. Per 1 million of CyT49 cells(ViaCyte), 4 μg of plasmid DNA was delivered along with the RNP.Electroporation was carried out as described in Example 2. Seven dayspost electroporation, the cells were enriched for PD-L1 positive cellsvia magnetic assisted cell sorting (MACS) using Miltenyi reagents(Anti-Mouse IgG MicroBeads Cat #130-048-401, LS Columns Cat#130-042-401, and MidiMACS Separator Cat #130-042-302) or Thermofisherreagents (DynaMag™-15 Magnet Cat #12301D, CELLection™ Pan Mouse IgG KitCat #11531D, Dynabeads™ Pan Mouse IgG Cat #11042).

After the enriched PD-L1 positive population was expanded, an HLA-Etrimer cDNA transgene was inserted into the TXNIP genomic locus viaCRISPR induced HDR using a donor plasmid comprising the HLA-E sequence.The HLA-E trimer cDNA was composed of a B2M signal peptide fused to anHLA-G presentation peptide fused to the B2M membrane protein fused tothe HLA-E protein without its signal peptide. This trimer design hasbeen previously published (Gornalusse et al. (2017) Nat. Biotechnol.35(8): 765-772). The HLA-E trimer coding sequence (including linkers) isSEQ ID NO: 55 (i.e., SEQ ID NOs: 26-31). The donor plasmid for HLA-Edelivery contains a CAGGS promoter driving expression of the HLA-Etrimer flanked by 800 base pair homology arms with identical sequence tothe TXNIP locus around exon 1 (FIG. 14, Table 10 and Table 11). In someembodiments, the donor plasmid comprises SEQ ID NO: 34 or 56.

TABLE 10 Elements of TXNIP-CAGGS-HLA-E Donor Plasmid 1 Element Location(size in bp) SEQ ID NO: Left ITR 1-130 (130)  6 LHA-TXNIP 145-944 (800)25 CMV enhancer 973-1352 (380)  8 chicken β-actin promoter 1355-1630(276)  9 chimeric intron 1631-2639 (1009) 10 B2M signal sequence2684-2743 (60) 26 HLA-G peptide 2744-2770 (27) 27 GS Linker 2771-2815(45) 28 B2M membrane protein 2816-3112 (297) 29 GS Linker 3113-3172 (60)30 HLA-E 3173-4183 (1011) 31 bGH poly(A) signal 4204-4428 (225) 12RHA-TXNIP 4435-5234 (800) 32 Right ITR 5276-5416 (141) 14 Entire Plasmid7763 bp 34

TABLE 11 Elements of TXNIP-CAGGS-HLA-E Donor Plasmid 2 Element Location(size in bp) SEQ ID NO: Left ITR 1-130 (130)  6 LHA-TXNIP 145-944 (800)25 CMV enhancer 973-1352 (380)  8 chicken β-actin promoter 1355-1630(276)  9 chimeric intron (truncated) 1631-2336 (706) 57 B2M signalsequence 2381-2440 (60) 26 HLA-G peptide 2441-2467 (27) 27 GS Linker2468-2512 (45) 28 B2M membrane protein 2513-2809 (297) 29 GS Linker2810-2869 (60) 30 HLA-E 2870-3880 (1011) 31 bGH poly(A) signal 3901-4125(225) 12 RHA-TXNIP 4132-4931 (800) 32 Right ITR 4973-5113 (141) 14Entire Plasmid 7460 bp 56

The TXNIP-T5 gRNA was used to facilitate insertion of the HLA-Etransgene at the targeted TXNIP locus. The HLA-E donor plasmid wasintroduced along with the RNP complex made up of the TXNIP-T5 gRNA andCas9 protein. Per 1 million of PD-L1+ cells, 4 μg of HLA-E donor plasmidDNA (SEQ ID NO: 56) was delivered along with the RNP. Alternatively,HLA-E donor plasmid DNA (SEQ ID NO: 34) can be used. Electroporation wascarried out as described in Example 2. Seven days post electroporation,the cells were enriched for HLA-E positive cells via MACS using Miltenyireagents or Thermofisher reagents. Post HLA-E enrichment, the cells weresingle-cell sorted using the WOLF FACS-sorter (Nanocellect) intoBIOLAMININ 521 CTG coated 96-well plates with StemFlex and Revitacell.Plated single cells were grown in a normoxia incubator (37° C., 8% CO₂)with every other day media changes until colonies were large enough tobe re-seeded as single cells. When confluent, samples were split formaintenance and genomic DNA extraction. The anti-PD-L1 and anti-HLA-Eantibodies (Table 4) were used for MACS enrichment and FACS-sorting into96-well plates with gating set for HLA-E and PD-L1 double positivecells. For FACS-sorting, unedited cells served as a negative control.

Correctly targeted clones were identified via PCR for the PD-L1 KIinsertion and the HLA-E KI insertion using primers that amplify a regionfrom outside the plasmid homology arms to the PD-L1 cDNA insertion orthe HLA-E cDNA insertion, respectively, enabling amplification of the KIintegrated DNA only. On-target insertion was tested for zygosity by PCRto assess if KI occurred in a heterozygous or homozygous manner. If aheterozygous clone was identified, the KI negative allele was sent forSanger sequencing to verify that it contained a B2M-disrupting indel ora TXNIP-disrupting indel, respectively. The correct KI clones with fullB2M and TXNIP disruptions (either via KI insertion or indel formation)were expanded in increasing tissue culture formats until a populationsize of 30 million cells was reached. Approximately 10 clones wereexpanded in this manner and confirmed to be pluripotent by testing forOCT4 and SOX2 via intracellular flow cytometry (FIG. 15).

Clones that passed the above tests, were then tested further forkaryotypic analysis (Cell Line Genetics), as described above. TheG-banding results of selected B2M KO/PD-L1 KI+TXNIP KO/HLA-E KI (“V1-B”)clones are shown in Table 12. Additionally, the V1-B clones were thentested for their competence to differentiate to pancreatic endodermprecursors (PEC).

TABLE 12 G-banding results Karyotyping FISH aCGH array Cell Line Passageanalysis analysis analysis V1-B003 P37 Normal Normal PASS V1-B007 P37Normal Normal PASS V1-B008 P36 Normal Normal PASS

PD-L1 and HLA-E continued to be expressed after differentiation to Stage6 cells per the previously reported pancreatic endocrine protocol(Rezania et al. (2014) Nat. Biotechnol. 32(11): 1121-1133) (FIG. 16).The population of differentiated cells is homogeneous in terms ofexpression of the transgene, e.g., 94.4% of the cells express PD-L1 and97.0% of the cells expression HLA-E. FIG. 22A shows similar morphologyof the various clone cells (“56-V1B-H9,” “S6-V1B-3B11,” “S6-V1B-1G7,”and “S6-V1B-3C2”) differentiated to Stage 6 compared to wild-type andnon-cutting guide control cells. Selected gene expression of B2MKO/PD-L1 KI and TXNIP KO/HLA-E KI clones are shown in FIGS. 23A-FIG.23F. The kinetic expression pattern of INS, NKX6.1, GCK, GCG, and SSTfrom B2M KO/PD-L1 KI and TXNIP KO/HLA-E KI clone cells was similar towild type cells (FIG. 23A). The expression levels of Stage 6 markers INS(FIG. 23B), NKX6.1 (FIG. 23C), GCG (FIG. 23D), SST (FIG. 23E), and GCK(FIG. 23F) from various differentiated B2M KO/PD-L1 KI and TXNIPKO/HLA-E KI clones (“S6-V1B-H9,” “S6-V1B-3B11,” “S6-V1B-1G7,” and“S6-V1B-3C2”) were similar to levels in Stage 6 wild-type cells andwild-type islets. An undifferentiated B2M KO/PD-L1 KI and TXNIP KO/HLA-EKI clone (“ES-V1B-H9”) was used as a negative control.

FIGS. 24A-24B show the flow cytometry assessment of INS and GCGexpression (FIG. 24A) and INS and NKX6.1 expression (FIG. 24B) in Stage6 cells differentiated from a B2M KO/PD-L1 KI and TXNIP KO/HLA-E KIclone. FIGS. 25A-25B show the percentage of INS expression (FIG. 25A)and NKX6.1 expression (FIG. 25B) in Stage 6 cells differentiated fromtwo B2M KO/PD-L1 KI and TXNIP KO/HLA-E KI clones (“56-V1B003” and“V1B-H9”). Expression in both was similar to that of wild-type andnon-cutting guide control cells.

At PECs stage, flow cytometry for chromogranin (CHGA), PDX1 and NKX6.1were performed. The heterogeneous population at PEC stage includepancreatic progenitors, early endocrine (FIG. 17). Targeted RNAseq forgene expression analysis was performed, as described above. Selectedgene expression for the TXNIP KO clone is shown in FIG. 18A and selectedgene expression for the V1-B clone is shown in FIG. 18B. The kineticexpression pattern of FOXA2, CHGA, PDX1 and NKX6.1 from V1-B or TXNIP KOclone cells was similar to wild type cells.

Cells were generated in which the HLA-E coding sequence was inserted inthe TXNIP locus (thereby knocking out the TXNIP gene) using the HLA-Edonor vector comprising the nucleotide sequence of SEQ ID NO: 56.Targeted RNAseq for gene expression analysis was performed, as describedabove. Selected gene expression for the TXNIP KO/HLA-E KI clone is shownin FIG. 28. The kinetic expression pattern of FOXA2, CHGA, PDX1 andNKX6.1 from TXNIP KO/HLA-E KI cells was similar to wild type cells.

Alternatively, cells were generated in which the HLA-E coding sequencewas inserted in the TXNIP locus using the HLA-E donor vector comprisingthe nucleotide sequence of SEQ ID NO: 34. Bulk edited cells weredifferentiated to PEC stage and expressed HLA-E in at least 75% of thepopulation of cells (data not shown). Flow cytometry assessment of PDX1and NKX6.1 expression in PEC cells differentiated from TXNIP KO cellswas similar to PEC cells differentiated from wild-type cells (data notshown).

Example 9: T-cell Activation/Proliferation Assay

PEC-differentiated cells were tested for their ability to trigger animmune response via in vitro human T-cell activation/proliferationassays. Fresh donor PBMCs were purchased from Hemacare and CD3+ T-cellswere purified using the Pan T-Cell Isolation Kit, human (Miltenyi Cat#130-096-535). The isolated T-cells were labeled with CellTrace™ CFSECell Proliferation Kit Protocol (Thermofisher Cat #C34554) permanufacturer instructions and co-incubated with differentiated PEC for 5days. Dynabeads™ Human T-Activator CD3/CD28 for T-Cell Expansion andActivation (Thermofisher Cat #11161D) were used as a positive control toactivate T-cells. T-cells alone were labeled with CFSE and used as anegative control. Percent of CD3+ CFSE+ cells was measured to assesspercent of T-cell proliferation (FIGS. 19A-19B). WT PEC triggered T-cellproliferation above T-cell alone control. B2M KO, B2M KO/PD-L1 KI, andB2M KO/PD-L1 KI+TXNIP KO/HLA-E KI CyT49-derived PEC did not triggerT-cell proliferation above T-cell only control showing the hypoimmunogenic nature of edited cells.

Example 10: In Vivo Efficacy Study of Gene Targeted Clonal Lines

Pancreatic endoderm cells were produced from CyT49-derived clonal hEScell lines with the following genetic modifications: 1) the targeteddeletion of B2M expression and forced expression of PD-L1, 2) thetargeted deletion of B2M expression and forced expression of HLA-E, or3) the targeted deletion TXNIP. In addition, a clonal un-modified cellline was obtained from transfection with a non-cutting guide-RNA (NCG).

Following standard procedures, pancreatic endoderm aggregates derivedfrom the indicated clonal lines were loaded into perforated devices (PD)to produce test or control articles. The PDs permit directvascularization upon subcutaneous transplantation, and the encapsulatedpancreatic progenitor cells mature in vivo into functional pancreaticendocrine cells including glucose-responsive, insulin-producing cells.

As summarized in Table 13, five groups of athymic nude rats wereimplanted subcutaneously with two articles, each containingapproximately 7×10⁶ pancreatic endoderm cells obtained fromdifferentiations of the four clonal lines described above, or wild-typeCyT49 hES (ViaCyte) cells.

TABLE 13 Study Design Genetic Modification Group Knock-out Knock-inNumber Num- Group hESC (Loss of (Gain of of End ber ID Origin Function)Function Animals Point 1 Control Un- None None 6 per 20 modified GroupWeeks CyT49 2 NCG CyT49 None None sub-clone 3 TXNIP CyT49 TXNIP None KOsub-clone 4 B2M CyT49 B2M PD-L1 KO/ sub-clone PD-L1 5 B2M CyT49 B2MHLA-E KO/ sub-clone HLA-E

Starting at 12 weeks all surviving animals were subjected to efficacyevaluation through glucose stimulated insulin secretion (GSIS) testing.Blood samples were obtained from non-fasted animals prior to and afterintraperitoneal administration of 3 g/kg glucose. Serum concentrationsof human C-peptide were determined through standard enzyme linkedimmunosorbent assays.

GSIS testing was performed at 12, 16, and 20 weeks. Results indicatedthere were no substantial differences between experimental groups,especially beyond the 12-week time point. Compared to the C-peptidelevels detected in the control group (Group 1, <40 pM to 2.0 nM, mean1.1 nM) C-peptide levels were elevated in 2 of 6 animals from Group 3(TXNIP KO, mean 1.5 nM). The other groups, Group 2 (NCG, mean 0.5 nM),Group 4 (B2M KO/PD-L1 KI, mean 0.5 nM), and Group 5 (B2M KO/HLA-E KI,mean 0.4 nM), presented a similar range of C-peptide levels compared tothe control group, but with more animals near the lower end of therange. However, these differences were not statistically significant.These results indicated that neither the genetic modifications that wereintroduced nor the manipulations required to generate clonal linesaffected the ability for the cell lines in question to differentiateinto pancreatic endoderm cells in vitro and subsequently generatefunctional beta cells in vivo.

At 20 weeks, after GSIS testing, animals were euthanized and explantedtest articles were fixed in neutral buffered formalin, processed toslides, and stained with H&E and by immunohistochemistry for insulin andglucagon.

In vivo efficacy evaluations through GSIS testing showed no substantialdifferences between unedited control articles and edited test articlesformulated with pancreatic endoderm cells derived from clonal cell lineseach carrying a subset of genetic modifications. The results suggest theindividual genetic modifications and the process by which they areintroduced may be tolerated in vivo.

Example 11. In Vivo Efficacy Study of B2M KO/PD-L1 KI, TXNIP KO/HLA-E KICell Lines

Four clonal lines were generated essentially as described above inExample 8 and loaded into perforated devices to form test articles.Control articles contained un-modified CyT49 cells (ViaCyte). Articlescomprising about 7×10⁶ pancreatic endoderm cells were subcutaneouslyimplanted into athymic nude rats (2 articles/rat, 8 rats/group).

At 12, 16, 20, and 24 weeks, all surviving animals were subjected toglucose stimulated insulin secretion (GSIS) testing. Blood samples wereobtained from fasted animals prior to and after intraperitonealadministration of 3 g/kg glucose. Serum concentrations of humanC-peptide were determined through standard enzyme linked immunosorbentassays. Serum C-peptide was detected in most animals at 12 weeks afterimplant. The serum C-peptide levels at 16, 20, and 24 weeks post implantare presented in Table 14. No statistically significant differences wereobserved between the groups of animals implanted with gene-edited versuscontrol cells.

TABLE 14 In vivo Serum C-peptide Levels. Serum C-peptide (pmol) GroupsMean Lower 95% Upper (95% Gene-edited cells-16 weeks 729 40 1418Gene-edited cells-20 weeks 1080 391 1769 Gene-edited cells-24 weeks 1676987 2365 Control cells-16 weeks 1075 386 1764 Control cells-20 weeks1883 1193 2572 Control cells-24 weeks 2466 1777 3155

At 25 weeks, surviving animals will be subjected to an insulin challenge(insulin tolerance test, ITT) to assess serum human C-peptide changes inresponse to diminishing blood glucose in the absence of access to food.Blood samples will be obtained from fasted animals prior to and atmultiple time points (15, 30, 60 minutes) after intraperitonealadministration of 1 unit of insulin per kg body weight. Serumconcentrations of human C-peptide will be determined through standardenzyme linked immunosorbent assays.

At 26 weeks, surviving animals will be euthanized and explanted testarticles will be processed to slides and stained with H&E and byimmunohistochemistry (IHC) for insulin and glucagon to identify humanpancreatic endocrine cells. Additional IHC for human-specific nuclearmarker NuMA1 will be performed to identify the potential location ofgraft-derived cells outside of the lumen of the test article explant.

Example 12. In Vivo Efficacy Study of B2M KO/PD-L1 KI, TXNIP KO/HLA-E KICell Line

Aggregates of B2M KO/PD-L1 KI, TXNIP KO/HLA-E KI pancreatic endodermcells (comprising approximately 7×10⁶ cells) will be formulated intotest articles. Forty-six athymic nude rats will be implantedsubcutaneously with two test articles each. Animals on study will beevaluated for GSIS, ITT, and non-fasting blood glucose (NFBG). Tenanimals per group will be euthanized at scheduled termination timepoints of 13, 17, 26, and 39 weeks, while 6 additional animals will beon study to account for possible early unscheduled terminations. Fromeach animal the two explanted test articles will be randomly assigned toeither histological evaluation or total C-peptide content assessment.Table 15 presents the study design.

TABLE 15 Study Design Number GSIS ITT of Number Time Time End Group Testof Points Points Point Explant Number Articles Animals (Weeks) (Weeks)(Weeks) Analyses 1 20 10 male 12 NA 13 For each 2 20 10 male 12,16 NA 17Group: 3 20 10 male 12, 16, 25 26 Histology 20, 24 5 animals 4 Up to Upto 12, 16, 20, 25, 33 39 C-peptide 32 16 male 24, 30, 36 content 5animals Total 92 46 male

At 12, 16, 20, 24, 30, and 36 weeks, all surviving animals will besubjected to efficacy evaluations through glucose stimulated insulinsecretion (GSIS) testing. Blood samples will be obtained from fastedanimals prior to and after intraperitoneal administration of 3 g/kgglucose. Serum concentrations of human C-peptide will be determinedthrough standard enzyme linked immunosorbent assays.

At 25 and 33 weeks, surviving animals will be subjected to an insulinchallenge (insulin tolerance test, ITT) to assess serum human C-peptidechanges in response to diminishing blood glucose in the absence ofaccess to food. Blood samples will be obtained from fasted animals priorto and multiple time points (15, 30, 60 minutes) after intraperitonealadministration of 1 unit of insulin per kg body weight. Serumconcentrations of human C-peptide will be determined through standardenzyme linked immunosorbent assays.

Non-fasting blood glucose (NFBG) will be measured prior to initiation offasting for GSIS and ITT testing, at approximately 12, 16, 20, 24, 25,30, 33, and 36 weeks.

At the scheduled end points identified in Table 13, animals will beeuthanized. Euthanasia will be performed by CO₂ inhalation followed bybilateral thoracotomy. Gross necropsy will be performed on all scheduledand unscheduled terminations and macroscopic abnormalities will berecorded.

Designated explants will be frozen followed by homogenization of lumencontent. Total C-peptide content of the homogenate will be determinedthrough standard enzyme linked immunosorbent assays. Total explantC-peptide content will be used to project clinical dosing.

Designated explanted test articles will be fixed in neutral bufferedformalin, processed to slides, and stained with H&E and byimmunohistochemistry (IHC) for insulin and glucagon to identify humanpancreatic endocrine cells. Additional IHC for human-specific nuclearmarker NuMA1 will be performed to identify the potential location ofgraft-derived cells outside of the lumen of the test article explant.

Example 13: Generation of B2M KO/PD-L1 KI, TXNIP KO/HLA-E KI in HumaniPSCs

Human iPSCs (iPSC 0025) were generated in which the PD-L1 codingsequence was inserted in the B2M locus. An RNP complex was formed bycombining B2M-2 gRNA (SEQ ID NO: 2) and Cas9 protein in molar ratio of3:1 (gRNA:Cas9). To form the RNP complex, gRNA and Cas9 were combined inone vessel with R-buffer to a total volume of 25 μL and incubated for 15min at RT. Cells were dissociated using ACCUTASE®, then resuspended inDMEM/F12 media (Gibco, cat #11320033), counted using an NC-200(Chemometec) and centrifuged. A total of 1×10⁶ cells were resuspendedwith the RNP complex. Four μg of the B2M-CAGGS-PD-L1 donor plasmid (SEQID NO: 33) and R-buffer were added for a total volume of 125 μL. Thismixture was then electroporated using the parameters: 2 pulses, 30 ms,1100 V. Seven days post electroporation, the cells were enriched forPD-L1 positive cells via MACS using Miltenyi reagents or Thermofisherreagents essentially as described above in Example 8.

After the enriched PD-L1 positive population was expanded, the cellswere electroporated with an RNP complex comprising TXNIP-T5 gRNA (SEQ IDNO: 20) and Cas9 protein in molar ratio of 3:1 (gRNA:Cas9) and 4 μg ofthe TXNIP-CAGGS-HLA-E donor plasmid 2 (SEQ ID NO: 56) essentially asdescribed above. Seven days post electroporation, the cells wereenriched for HLA-E positive cells via MACS using Miltenyi reagents orThermofisher reagents. Post HLA-E enrichment, the cells were single-cellsorted using the WOLF FACS-sorter (Nanocellect) into BIOLAMININ 521 CTGcoated 96-well plates with StemFlex and Revitacell. Plated single cellswere grown in a normoxia incubator (37° C., 8% CO₂) with every other daymedia changes until colonies were large enough to be re-seeded as singlecells. When confluent, samples were split for maintenance and genomicDNA extraction. The anti-PD-L1 and anti-HLA-E antibodies (Table 4) wereused for MACS enrichment and FACS-sorting into 96-well plates withgating set for HLA-E and PD-L1 double positive cells. For FACS-sorting,unedited cells served as a negative control.

Correctly targeted clones were identified via PCR for the PD-L1 KIinsertion and the HLA-E KI insertion using primers that amplify a regionfrom outside the plasmid homology arms to the PD-L1 cDNA insertion orthe HLA-E cDNA insertion, respectively, enabling amplification of the KIintegrated DNA only. On-target insertion was tested for zygosity by PCRto assess if KI occurred in a heterozygous or homozygous manner. If aheterozygous clone was identified, the KI negative allele was sent forSanger sequencing to verify that it contained a B2M-disrupting indel ora TXNIP-disrupting indel, respectively. The correct KI clones with fullB2M and TXNIP disruptions (either via KI insertion or indel formation)were expanded in increasing tissue culture formats until a populationsize of 30 million cells was reached. Selected clones were expanded inthis manner and confirmed to be pluripotent by testing for OCT4 and SOX2via intracellular flow cytometry.

Four edited hiPSCs clones (VI-B) were differentiated using thepancreatic endocrine protocol of Rezania et al. (Nat Biotechnol. 2014November; 32(11):1121-33). At Stage 4, flow cytometry for chromogranin(CHGA), PDX1 and NKX6.1 was performed. The results for PDX1 and NKX6.1of a clone (clone 1) seeded at different representative densities isshown in FIG. 26A. CHGA was negative for all four clones. Flow cytometryfor PD-L1 and HLA-E was also performed. The results for PD-L1 and HLA-Eof a clone (clone 1) is shown in FIG. 26B.

Example 14: Process for Manufacturing B2M KO/PD-L1 KI, TXNIP KO/HLA-E KIHuman Pluripotent Stem Cells (hPSCs) Cryo Cell Banks

CyT49 hESCs (ViaCyte) were electroporated with an RNP complex comprisingB2M-2 gRNA (SEQ ID NO: 2) and Cas9 protein in molar ratio of 3:1(gRNA:Cas9) and 4 μg of the B2M-CAGGS-PD-L1 donor plasmid (SEQ ID NO:33) for 2 pulses of 30 ms at 1100 V. Following electroporation, thecells were pipetted out into an Eppendorf tube filled with StemFlexmedia with RevitaCell. This cell suspension was then plated into tissueculture dishes pre-coated with BIOLAMININ 521 CTG at 1:20 dilution.Cells were cultured in a normoxia incubator (37° C., 8% CO₂).

Seven days post electroporation, the cells were enriched for PD-L1positive cells via MACS using Alexa-488 labeled anti-PD-L1 antibodiesand magnetic beads (DYNABEADS® Pan Mouse IgG; Thermo Fisher). The PD-L1positive cells were expanded by culturing in XF-KSR expansion media(Gibco) for 7 days.

The PD-L1 positive cells were then electroporated with an RNP complexcomprising TXNIP-T5 gRNA (SEQ ID NO: 20) and Cas9 protein in molar ratioof 3:1 (gRNA:Cas9) and 4 of the TXNIP-CAGGS-HLA-E donor plasmid 2 (SEQID NO: 56) for 2 pulses of 30 ms at 1100 V. Following electroporation,the cells were pipetted out into an Eppendorf tube filled with StemFlexmedia with RevitaCell. This cell suspension was then plated into tissueculture dishes pre-coated with BIOLAMININ 521 CTG at 1:20 dilution.Cells were cultured in a normoxia incubator (37° C., 8% CO₂).

Seven days post electroporation, the cells were enriched for HLA-Epositive cells via MACS using PE-labeled anti-HLA-E antibodies andmagnetic beads (DYNABEADS® Pan Mouse IgG; Thermo Fisher). The PD-L1 andHLA-E double positive cells were expanded by culturing in XF-KSRexpansion media (Gibco) for about 5 days.

The PD-L1 and HLA-E double positive cells were single cell sorted. Forthis, the cells were fed with StemFlex Complete with Revitacell (forfinal concentration of 1× Revitacell) 3-4 hours prior to dissociationwith ACCUTASE®. Following dissociation, single cells were sorted intosingle wells of BIOLAMININ coated 96 well tissue culture plate. The WOLFFACS-sorter (Nanocellect) was used to sort single cells into the wellsusing the anti-PD-L1 and anti-HLA-E antibodies described above. Theplates were pre-filled with 100-200 μL of StemFlex Complete withRevitacell. Three days post cell seeding, the cells were fed with freshStemFlex and continued to be fed every other day with 100-200 μL ofmedia. After 10 days of growth, the cells were fed daily with StemFlexuntil day 12-14. At this time, the plates were dissociated withACCUTASE® and the collected cell suspensions were split 1:2 into two 96well plates, which were cultured for about 4 days.

A portion of the cells were harvested for visual analysis (morphology)and DNA analysis (PCR and DNA sequencing for zygosity analysis and indelprofile), and the remainder of the cells were cultured and expanded forculturing in T175 flasks. After about two weeks of culturing, cloneswere selected for freezing. The cells were characterized before andafter freezing for morphology, viability, endotoxins, mycoplasma,karyotype, pluripotency, differentiation capacity, on/off targetanalysis, random plasmid integration, residual Cas9/plasmid usingstandard procedures. The cells were frozen in cryo media and stored incryo vials at −80° C. or liquid nitrogen.

A particular B2M KO/PD-L1 KI+TXNIP KO/HLA-E KI clone (“seed clone”) wasmanufactured and isolated by said process. The seed clone wasdifferentiated to PEC stage and characterized. FIG. 27A shows themorphology of the seed clone at the PEC stage was similar to wild typecells. FIG. 27B shows the kinetic expression pattern of FOXA2, CHGA,PDX1 and NKX6.1 over a differentiation time course in cellsdifferentiated from the seed clone was similar to wild type cells. FIG.27C shows the percentage of CHGA®/NKX6.1⁺/PDX1⁺ cells in thedifferentiated population.

The invention claimed is:
 1. An in vitro method for generating auniversal donor cell, the method comprising delivering to a stem cell:(a) ribonucleoprotein (RNP) complex comprising an RNA-guided nucleaseand a guide RNA (gRNA) targeting a target site in a thioredoxininteracting protein (TXNIP) gene locus; and (b) a vector comprising anucleic acid, the nucleic acid comprising: (i) a nucleotide sequenceencoding HLA class I histocompatibility antigen, alpha chain E (HLA-E);(ii) a nucleotide sequence consisting of SEQ ID NO: 25 having sequencehomology with a genomic region located left of the target site in theTXNIP gene locus; and (iii) a nucleotide sequence consisting of SEQ IDNO: 32 having sequence homology with a genomic region located right ofthe target site in the TXNIP gene locus, wherein (i) is flanked by (ii)and (iii); wherein the TXNIP gene locus is cleaved at the target siteand the nucleotide sequence encoding HLA-E is inserted into the TXNIPgene locus, thereby disrupting the TXNIP gene locus and generating auniversal donor cell, wherein the universal donor cell has increasedimmune evasion and/or cell survival compared to a control cell.
 2. Thein vitro method of claim 1, wherein the stem cell is an embryonic stemcell, an adult stem cell, an induced pluripotent stem cell, or ahematopoietic stem cell.
 3. The in vitro method of claim 1, wherein thestem cell is a human stem cell.
 4. The in vitro method of claim 1,wherein the RNA-guided nuclease is a Cas9 nuclease.
 5. The in vitromethod of claim 4, wherein the Cas9 nuclease is linked to at least onenuclear localization signal.
 6. The in vitro method of claim 1, whereinthe gRNA comprises a spacer sequence corresponding to a sequenceconsisting of any one of SEQ ID NO: 16-20.
 7. The in vitro method ofclaim 1, wherein the gRNA comprises a spacer sequence corresponding to asequence consisting of SEQ ID NO:
 20. 8. The in vitro method of claim 1,wherein the nucleotide sequence encoding HLA-E consists essentially ofSEQ ID NO:
 55. 9. The in vitro method of claim 8, wherein SEQ ID NO: 55comprises a sequence encoding a B2M signal peptide, a sequence encodingan HLA-G presentation peptide, a sequence encoding a B2M membraneprotein, and a sequence encoding HLA-E without its signal peptide. 10.The in vitro method of claim 1, wherein the nucleotide sequence encodingHLA-E is operably linked to an exogenous promoter.
 11. The in vitromethod of claim 10, wherein the exogenous promoter is a CAG promotercomprising a CMV enhancer, a (β-actin promoter, and a chimeric intron.12. The in vitro method of claim 1, wherein the vector consistsessentially of SEQ ID NO: 34 or SEQ ID NO:
 56. 13. The in vitro methodof claim 1, wherein the disrupting the TXNIP gene locus leads to reducedor eliminated expression of TXNIP.
 14. The in vitro method of claim 1,wherein the universal donor cells expresses HLA-E but does not expressTXNIP.
 15. The in vitro method of claim 1, wherein the control cell is awild type cell or a cell that does not comprise the nucleotide sequenceencoding HLA-E inserted into the TXNIP gene locus.
 16. The in vitromethod of claim 1, wherein: the gRNA comprises a spacer sequencecorresponding to a sequence consisting of SEQ ID NO: 20; and thenucleotide sequence encoding HLA-E consists essentially of SEQ ID NO:55.
 17. The in vitro method of claim 16, wherein SEQ ID NO: 55 isoperably linked to an exogenous promoter.
 18. The in vitro method ofclaim 17, wherein the exogenous promoter is a CAG promoter comprising aCMV enhancer, a (β-actin promoter, and a chimeric intron.
 19. An invitro method for generating a universal donor cell, the methodcomprising delivering to a stem cell: (a) ribonucleoprotein (RNP)complex comprising an RNA-guided nuclease and a guide RNA (gRNA)targeting a target site in a thioredoxin interacting protein (TXNIP)gene locus; and (b) a vector comprising a nucleic acid, the nucleic acidcomprising: (i) a nucleotide sequence encoding HLA class Ihistocompatibility antigen, alpha chain E (HLA-E) consisting essentiallyof SEQ ID NO: 55; (ii) a nucleotide sequence having sequence homologywith a genomic region located left of the target site in the TXNIP genelocus; and (iii) a nucleotide sequence having sequence homology with agenomic region located right of the target site in the TXNIP gene locus,wherein (i) is flanked by (ii) and (iii); wherein the TXNIP gene locusis cleaved at the target site and the nucleotide sequence encoding HLA-Eis inserted into the TXNIP gene locus, thereby disrupting the TXNIP genelocus and generating a universal donor cell, wherein the universal donorcell has increased immune evasion and/or cell survival compared to acontrol cell.
 20. The in vitro method of claim 19, wherein SEQ ID NO: 55comprises a sequence encoding a B2M signal peptide, a sequence encodingan HLA-G presentation peptide, a sequence encoding a B2M membraneprotein, and a sequence encoding HLA-E without its signal peptide. 21.The in vitro method of claim 19, wherein the stem cell is an embryonicstem cell, an adult stem cell, an induced pluripotent stem cell, or ahematopoietic stem cell; and/or wherein the stem cell is a human stemcell.
 22. The in vitro method of claim 19, wherein the RNA-guidednuclease is a Cas9 nuclease.
 23. The in vitro method of claim 22,wherein the Cas9 nuclease is linked to at least one nuclear localizationsignal.
 24. The in vitro method of claim 19, wherein the nucleotidesequence encoding HLA-E is operably linked to an exogenous promoter. 25.The in vitro method of claim 24, wherein the exogenous promoter is a CAGpromoter comprising a CMV enhancer, a (β-actin promoter, and a chimericintro.
 26. The in vitro method of claim 19, wherein the gRNA comprises aspacer sequence corresponding to a sequence consisting of any one of SEQID NO: 16-20.
 27. The in vitro method of claim 19, wherein thenucleotide sequence having sequence homology with the genomic regionlocated left of the target site in the TXNIP gene locus consistsessentially of SEQ ID NO: 25 and/or the nucleotide sequence havingsequence homology with the genomic region located right of the targetsite in the TXNIP gene locus consists essentially of SEQ ID NO:
 32. 28.The in vitro method of claim 19, wherein: the gRNA comprises a spacersequence corresponding to a sequence consisting of SEQ ID NO: 20; thenucleotide sequence having sequence homology with the genomic regionlocated left of the target site in the TXNIP gene locus consistsessentially of SEQ ID NO: 25; and the nucleotide sequence havingsequence homology with the genomic region located right of the targetsite in the TXNIP gene locus consists essentially of SEQ ID NO: 32.